Electropherograms are commonly used to sequence portions of genomes.
An image of the 46 chromosomes, making up the diploid genome of human male. (The mitochondrial chromosome is not shown.)
Whole genome sequencing (also known as WGS, full genome sequencing, complete genome sequencing, or entire genome sequencing) is ostensibly the process of determining the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. In practice, genome sequences that are nearly complete are also called whole genome sequences.
Whole genome sequencing has largely been used as a research tool, but is currently being introduced to clinics. In the future of personalized medicine, whole genome sequence data will be an important tool to guide therapeutic intervention. The tool of gene sequencing at SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response.
Whole genome sequencing should not be confused with DNA profiling,
which only determines the likelihood that genetic material came from a
particular individual or group, and does not contain additional
information on genetic relationships, origin or susceptibility to
specific diseases.
In addition, whole genome sequencing should not be confused with
methods that sequence specific subsets of the genome - such methods
include whole exome sequencing (1% of the genome) or SNP genotyping (less than 0.1% of the genome).
As of 2017 there were no complete genomes for any mammals, including humans. Between 4% to 9% of the human genome, mostly satellite DNA, had not been sequenced.
The genome of the lab mouse Mus musculus was published in 2002.
It took 10 years and 50 scientists spanning the globe to sequence the genome of Elaeis guineensis (oil palm). This genome was particularly difficult to sequence because it had many repeated sequences which are difficult to organise.
The DNA sequencing methods used in the 1970s and 1980s were manual, for example Maxam-Gilbert sequencing and Sanger sequencing. The shift to more rapid, automated sequencing methods in the 1990s finally allowed for sequencing of whole genomes.
The first organism to have its entire genome sequenced was Haemophilus influenzae in 1995. After it, the genomes of other bacteria and some archaea were first sequenced, largely due to their small genome size. H. influenzae has a genome of 1,830,140 base pairs of DNA. In contrast, eukaryotes, both unicellular and multicellular such as Amoeba dubia and humans (Homo sapiens) respectively, have much larger genomes (see C-value paradox). Amoeba dubia has a genome of 700 billion nucleotide pairs spread across thousands of chromosomes. Humans contain fewer nucleotide pairs (about 3.2 billion in each germ cell - note the exact size of the human genome is still being revised) than A. dubia however their genome size far outweighs the genome size of individual bacteria.
The first bacterial and archaeal genomes, including that of H. influenzae, were sequenced by Shotgun sequencing. In 1996 the first eukaryotic genome (Saccharomyces cerevisiae) was sequenced. S. cerevisiae, a model organism in biology has a genome of only around 12 million nucleotide pairs, and was the first unicellular eukaryote to have its whole genome sequenced. The first multicellular eukaryote, and animal, to have its whole genome sequenced was the nematode worm: Caenorhabditis elegans in 1998.
Eukaryotic genomes are sequenced by several methods including Shotgun
sequencing of short DNA fragments and sequencing of larger DNA clones
from DNA libraries such as bacterial artificial chromosomes (BACs) and yeast artificial chromosomes (YACs).
In 1999, the entire DNA sequence of human chromosome 22, the shortest human autosome, was published. By the year 2000, the second animal and second invertebrate (yet first insect) genome was sequenced - that of the fruit fly Drosophila melanogaster - a popular choice of model organism in experimental research. The first plant genome - that of the model organism Arabidopsis thaliana - was also fully sequenced by 2000. By 2001, a draft of the entire human genome sequence was published. The genome of the laboratory mouse Mus musculus was completed in 2002.
In 2004, the Human Genome Project published an incomplete version of the human genome.
Almost any biological sample containing a full copy of the DNA—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing. Such samples may include saliva, epithelial cells, bone marrow, hair (as long as the hair contains a hair follicle), seeds, plant leaves, or anything else that has DNA-containing cells.
The genome sequence of a single cell selected from a mixed population of cells can be determined using techniques of single cell genome sequencing.
This has important advantages in environmental microbiology in cases
where a single cell of a particular microorganism species can be
isolated from a mixed population by microscopy on the basis of its
morphological or other distinguishing characteristics. In such cases the
normally necessary steps of isolation and growth of the organism in
culture may be omitted, thus allowing the sequencing of a much greater
spectrum of organism genomes.
An ABI PRISM 3100 Genetic Analyzer. Such capillary sequencers automated the early efforts of sequencing genomes.
Sequencing of nearly an entire human genome was first accomplished in 2000 partly through the use of shotgun sequencing technology. While full genome shotgun sequencing for small (4000–7000 base pair) genomes was already in use in 1979, broader application benefited from pairwise end sequencing, known colloquially as double-barrel shotgun sequencing.
As sequencing projects began to take on longer and more complicated
genomes, multiple groups began to realize that useful information could
be obtained by sequencing both ends of a fragment of DNA. Although
sequencing both ends of the same fragment and keeping track of the
paired data was more cumbersome than sequencing a single end of two
distinct fragments, the knowledge that the two sequences were oriented
in opposite directions and were about the length of a fragment apart
from each other was valuable in reconstructing the sequence of the
original target fragment.
The first published description of the use of paired ends was in 1990 as part of the sequencing of the human HPRT locus,
although the use of paired ends was limited to closing gaps after the
application of a traditional shotgun sequencing approach. The first
theoretical description of a pure pairwise end sequencing strategy,
assuming fragments of constant length, was in 1991. In 1995 the innovation of using fragments of varying sizes was introduced,
and demonstrated that a pure pairwise end-sequencing strategy would be
possible on large targets. The strategy was subsequently adopted by The Institute for Genomic Research (TIGR) to sequence the entire genome of the bacterium Haemophilus influenzae in 1995, and then by Celera Genomics to sequence the entire fruit fly genome in 2000, and subsequently the entire human genome. Applied Biosystems, now called Life Technologies, manufactured the automated capillary sequencers utilized by both Celera Genomics and The Human Genome Project.
Current techniques
While capillary sequencing was the first approach to successfully
sequence a nearly full human genome, it is still too expensive and takes
too long for commercial purposes. Since 2005 capillary sequencing has
been progressively displaced by high-throughput (formerly "next-generation") sequencing technologies such as Illumina dye sequencing, pyrosequencing, and SMRT sequencing. All of these technologies continue to employ the basic shotgun
strategy, namely, parallelization and template generation via genome
fragmentation.
Other technologies are emerging, including nanopore technology.
Though nanopore sequencing technology is still being refined, its
portability and potential capability of generating long reads are of
relevance to whole-genome sequencing applications.
Analysis
In principle, full genome sequencing can provide the raw nucleotide
sequence of an individual organism's DNA. However, further analysis
must be performed to provide the biological or medical meaning of this
sequence, such as how this knowledge can be used to help prevent
disease. Methods for analysing sequencing data are being developed and
refined.
Because sequencing generates a lot of data (for example, there are approximately six billion base pairs
in each human diploid genome), its output is stored electronically and
requires a large amount of computing power and storage capacity.
While analysis of WGS data can be slow, it is possible to speed up this step by using dedicated hardware.
Commercialization
Total cost of sequencing a whole human genome as calculated by the NHGRI.
A commonly-referenced commercial target for sequencing cost is the $1,000 genome.
Incentive
In October 2006, the X Prize Foundation, working in collaboration with the J. Craig Venter Science Foundation, established the Archon X Prize for Genomics,
intending to award $10 million to "the first team that can build a
device and use it to sequence 100 human genomes within 10 days or less,
with an accuracy of no more than one error in every 1,000,000 bases
sequenced, with sequences accurately covering at least 98% of the
genome, and at a recurring cost of no more than $1,000 per genome".
The Archon X Prize for Genomics was cancelled in 2013, before its official start date.
History
In 2007, Applied Biosystems started selling a new type of sequencer called SOLiD System. The technology allowed users to sequence 60 gigabases per run.
In June 2009, Illumina announced that they were launching their own Personal Full Genome Sequencing Service at a depth of 30× for $48,000 per genome.
In August 2009, the founder of Helicos Biosciences, Stephen Quake, stated that using the company's Single Molecule Sequencer he sequenced his own full genome for less than $50,000.
In November 2009, Complete Genomics published a peer-reviewed paper in Science demonstrating its ability to sequence a complete human genome for $1,700.
In May 2011, Illumina lowered its Full Genome Sequencing service to $5,000 per human genome, or $4,000 if ordering 50 or more.
Helicos Biosciences, Pacific Biosciences, Complete Genomics, Illumina,
Sequenom, ION Torrent Systems, Halcyon Molecular, NABsys, IBM, and GE
Global appear to all be going head to head in the race to commercialize
full genome sequencing.
With sequencing costs declining, a number of companies began
claiming that their equipment would soon achieve the $1,000 genome:
these companies included Life Technologies in January 2012, Oxford Nanopore Technologies in February 2012 and Illumina in February 2014. As of 2015, the NHGRI estimates the cost of obtaining a whole-genome sequence at around $1,500.
In 2016, Veritas Corp. began selling whole gene sequencing,
including a report as to some of the information in the sequencing for
$999. Effective use of whole gene sequencing can cost considerably more. Note, also, that there remain parts of the human genome that have not been fully sequenced.
Comparison with other technologies
DNA microarrays
Full genome sequencing provides information on a genome that is orders of magnitude larger than by DNA arrays, the previous leader in genotyping technology.
For humans, DNA arrays currently provide genotypic information on up to one million genetic variants,
while full genome sequencing will provide information on all six
billion bases in the human genome, or 3,000 times more data. Because of
this, full genome sequencing is considered a disruptive innovation
to the DNA array markets as the accuracy of both range from 99.98% to
99.999% (in non-repetitive DNA regions) and their consumables cost of
$5000 per 6 billion base pairs is competitive (for some applications)
with DNA arrays ($500 per 1 million basepairs).
Applications
Mutation frequencies
Whole genome sequencing has established the mutation
frequency for whole human genomes. The mutation frequency in the whole
genome between generations for humans (parent to child) is about 70 new
mutations per generation.
An even lower level of variation was found comparing whole genome
sequencing in blood cells for a pair of monozygotic (identical twins)
100-year-old centenarians. Only 8 somatic differences were found, though somatic variation occurring in less than 20% of blood cells would be undetected.
In the specifically protein coding regions of the human genome,
it is estimated that there are about 0.35 mutations that would change
the protein sequence between parent/child generations (less than one
mutated protein per generation).
In cancer, mutation frequencies are much higher, due to genome instability.
This frequency can further depend on patient age, exposure to DNA
damaging agents (such as UV-irradiation or components of tobacco smoke)
and the activity/inactivity of DNA repair mechanisms.
Furthermore, mutation frequency can vary between cancer types: in
germline cells, mutation rates occur at approximately 0.023 mutations
per megabase, but this number is much higher in breast cancer (1.18-1.66
somatic mutations per Mb), in lung cancer (17.7) or in melanomas (~33). Since the haploid human genome consists of approximately 3,200 megabases, this translates into about 74 mutations (mostly in noncoding
regions) in germline DNA per generation, but 3,776-5,312 somatic
mutations per haploid genome in breast cancer, 56,640 in lung cancer and
105,600 in melanomas.
The distribution of somatic mutations across the human genome is very uneven,
such that the gene-rich, early-replicating regions receive fewer
mutations than gene-poor, late-replicating heterochromatin, likely due
to differential DNA repair activity. In particular, the histone modification H3K9me3 is associated with high, and H3K36me3 with low mutation frequencies.
Genome-wide association studies
In research, whole-genome sequencing can be used in a Genome-Wide
Association Study (GWAS) - a project aiming to determine the genetic
variant or variants associated with a disease or some other phenotype.
Diagnostic use
In 2009, Illumina released its first whole genome sequencers that were approved for clinical as opposed to research-only use and doctors at academic medical centers began quietly using them to try to diagnose what was wrong with people whom standard approaches had failed to help.
The price to sequence a genome at that time was US$19,500, which was
billed to the patient but usually paid for out of a research grant; one
person at that time had applied for reimbursement from their insurance
company.
For example, one child had needed around 100 surgeries by the time he
was three years old, and his doctor turned to whole genome sequencing to
determine the problem; it took a team of around 30 people that included
12 bioinformatics
experts, three sequencing technicians, five physicians, two genetic
counsellors and two ethicists to identify a rare mutation in the XIAP that was causing widespread problems.
Currently available newborn screening
for childhood diseases allows detection of rare disorders that can be
prevented or better treated by early detection and intervention.
Specific genetic tests
are also available to determine an etiology when a child's symptoms
appear to have a genetic basis. Full genome sequencing, in addition has
the potential to reveal a large amount of information (such as carrier status for autosomal recessive disorders, genetic risk factors for complex
adult-onset diseases, and other predictive medical and non-medical
information) that is currently not completely understood, may not be
clinically useful to the child during childhood, and may not necessarily
be wanted by the individual upon reaching adulthood.
Due to recent cost reductions (see above) whole genome sequencing
has become a realistic application in DNA diagnostics. In 2013, the
3Gb-TEST consortium obtained funding from the European Union to prepare
the health care system for these innovations in DNA diagnostics. Quality assessment schemes, Health technology assessment and guidelines
have to be in place. The 3Gb-TEST consortium has identified the
analysis and interpretation of sequence data as the most complicated
step in the diagnostic process. At the Consortium meeting in Athens in September 2014, the Consortium coined the word genotranslation for this crucial step. This step leads to a so-called genoreport. Guidelines are needed to determine the required content of these reports.
Genomes2People (G2P), an initiative of Brigham and Women's Hospital and Harvard Medical School was created in 2011 to examine the integration of genomic sequencing into clinical care of adults and children. G2P's director, Robert C. Green,
had previously led the REVEAL study — Risk Evaluation and Education for
Alzheimer’s Disease – a series of clinical trials exploring patient
reactions to the knowledge of their genetic risk for Alzheimer’s.
Ethical concerns
The introduction of whole genome sequencing may have ethical implications.
On one hand, genetic testing can potentially diagnose preventable
diseases, both in the individual undergoing genetic testing and in their
relatives. On the other hand, genetic testing has potential downsides such as genetic discrimination, loss of anonymity, and psychological impacts such as discovery of non-paternity.
Some ethicists insist that the privacy of individuals undergoing genetic testing must be protected. Indeed, privacy issues can be of particular concern when minors undergo genetic testing.
Illumina's CEO, Jay Flatley, claimed in February 2009 that "by 2019 it
will have become routine to map infants' genes when they are born". This potential use of genome sequencing is highly controversial, as it runs counter to established ethicalnorms for predictive genetic testing of asymptomatic minors that have been well established in the fields of medical genetics and genetic counseling.
The traditional guidelines for genetic testing have been developed over
the course of several decades since it first became possible to test
for genetic markers associated with disease, prior to the advent of
cost-effective, comprehensive genetic screening.
When an individual undergoes whole genome sequencing, they reveal
information about not only their own DNA sequences, but also about
probable DNA sequences of their close genetic relatives. This information can further reveal useful predictive information about relatives' present and future health risks.
Hence, there are important questions about what obligations, if any,
are owed to the family members of the individuals who are undergoing
genetic testing. In Western/European society, tested individuals are
usually encouraged to share important information on any genetic
diagnoses with their close relatives, since the importance of the
genetic diagnosis for offspring and other close relatives is usually one
of the reasons for seeking a genetic testing in the first place.
Nevertheless, a major ethical dilemma can develop when the patients
refuse to share information on a diagnosis that is made for serious
genetic disorder that is highly preventable and where there is a high
risk to relatives carrying the same disease mutation. Under such
circumstances, the clinician may suspect that the relatives would rather
know of the diagnosis and hence the clinician can face a conflict of
interest with respect to patient-doctor confidentiality.
Privacy concerns can also arise when whole genome sequencing is
used in scientific research studies. Researchers often need to put
information on patient's genotypes and phenotypes into public scientific
databases, such as locus specific databases.
Although only anonymous patient data are submitted to locus specific
databases, patients might still be identifiable by their relatives in
the case of finding a rare disease or a rare missense mutation.
People with public genome sequences
The first nearly complete human genomes sequenced were two Americans of predominantly Northwestern European ancestry in 2007 (J. Craig Venter at 7.5-fold coverage, and James Watson at 7.4-fold). This was followed in 2008 by sequencing of an anonymous Han Chinese man (at 36-fold), a Yoruban man from Nigeria (at 30-fold), and a female caucasian Leukemia patient (at 33 and 14-fold coverage for tumor and normal tissues). Steve Jobs was among the first 20 people to have their whole genome sequenced, reportedly for the cost of $100,000. As of June 2012, there were 69 nearly complete human genomes publicly available. In November 2013, a Spanish family made their personal genomics data publicly available under a Creative Commons public domain license. The work was led by Manuel Corpas and the data obtained by direct-to-consumer genetic testing with 23andMe and the Beijing Genomics Institute). This is believed to be the first such public genomics dataset for a whole family.
Medical genetics is the branch of medicine that involves the diagnosis and management of hereditary disorders. Medical genetics differs from human genetics
in that human genetics is a field of scientific research that may or
may not apply to medicine, while medical genetics refers to the
application of genetics to medical care. For example, research on the
causes and inheritance of genetic disorders
would be considered within both human genetics and medical genetics,
while the diagnosis, management, and counselling people with genetic
disorders would be considered part of medical genetics.
In contrast, the study of typically non-medical phenotypes
such as the genetics of eye color would be considered part of human
genetics, but not necessarily relevant to medical genetics (except in
situations such as albinism). Genetic medicine is a newer term for medical genetics and incorporates areas such as gene therapy, personalized medicine, and the rapidly emerging new medical specialty, predictive medicine.
In
some ways, many of the individual fields within medical genetics are
hybrids between clinical care and research. This is due in part to
recent advances in science and technology that have enabled an unprecedented understanding of genetic disorders.
In the United States, physicians who practice clinical genetics
are accredited by the American Board of Medical Genetics and Genomics
(ABMGG).
In order to become a board-certified practitioner of Clinical Genetics,
a physician must complete a minimum of 24 months of training in a
program accredited by the ABMGG. Individuals seeking acceptance into
clinical genetics training programs must hold an M.D. or D.O. degree (or
their equivalent) and have completed a minimum of 24 months of training
in an ACGME-accredited residency program in internal medicine, pediatrics, obstetrics and gynecology, or other medical specialty.
Mitochondrial genetics concerns the diagnosis and management of mitochondrial disorders, which have a molecular basis but often result in biochemical abnormalities due to deficient energy production.
There exists some overlap between medical genetic diagnostic laboratories and molecular pathology.
Genetic counseling
Genetic
counseling is the process of providing information about genetic
conditions, diagnostic testing, and risks in other family members,
within the framework of nondirective counseling. Genetic counselors
are non-physician members of the medical genetics team who specialize
in family risk assessment and counseling of patients regarding genetic
disorders. The precise role of the genetic counselor varies somewhat
depending on the disorder.
History
Although genetics has its roots back in the 19th century with the work of the Bohemian monk Gregor Mendel
and other pioneering scientists, human genetics emerged later. It
started to develop, albeit slowly, during the first half of the 20th
century. Mendelian (single-gene) inheritance was studied in a number of
important disorders such as albinism, brachydactyly (short fingers and toes), and hemophilia. Mathematical approaches were also devised and applied to human genetics. Population genetics was created.
Medical genetics was a late developer, emerging largely after the close of World War II (1945) when the eugenics
movement had fallen into disrepute. The Nazi misuse of eugenics sounded
its death knell. Shorn of eugenics, a scientific approach could be used
and was applied to human and medical genetics. Medical genetics saw an
increasingly rapid rise in the second half of the 20th century and
continues in the 21st century.
Current practice
The
clinical setting in which patients are evaluated determines the scope
of practice, diagnostic, and therapeutic interventions. For the
purposes of general discussion, the typical encounters between patients
and genetic practitioners may involve:
Referral to an out-patient genetics clinic (pediatric, adult, or
combined) or an in-hospital consultation, most often for diagnostic
evaluation.
Referral for counseling in a prenatal genetics clinic to discuss risks to the pregnancy (advanced maternal age,
teratogen exposure, family history of a genetic disease), test results
(abnormal maternal serum screen, abnormal ultrasound), and/or options
for prenatal diagnosis (typically non-invasive prenatal screening,
diagnostic amniocentesis or chorionic villus sampling).
Multidisciplinary specialty clinics that include a clinical
geneticist or genetic counselor (cancer genetics, cardiovascular
genetics, craniofacial or cleft lip/palate, hearing loss clinics,
muscular dystrophy/neurodegenerative disorder clinics).
Diagnostic evaluation
Each
patient will undergo a diagnostic evaluation tailored to their own
particular presenting signs and symptoms. The geneticist will establish
a differential diagnosis and recommend appropriate testing. These tests might evaluate for chromosomal disorders, inborn errors of metabolism, or single gene disorders.
Chromosome studies
Chromosome
studies are used in the general genetics clinic to determine a cause
for developmental delay/mental retardation, birth defects, dysmorphic
features, and/or autism. Chromosome analysis is also performed in the
prenatal setting to determine whether a fetus is affected with
aneuploidy or other chromosome rearrangements. Finally, chromosome
abnormalities are often detected in cancer samples. A large number of
different methods have been developed for chromosome analysis:
Chromosome analysis using a karyotype involves special stains that generate light and dark bands, allowing identification of each chromosome under a microscope.
Fluorescence in situ hybridization
(FISH) involves fluorescent labeling of probes that bind to specific
DNA sequences, used for identifying aneuploidy, genomic deletions or
duplications, characterizing chromosomal translocations and determining
the origin of ring chromosomes.
Chromosome painting is a technique that uses fluorescent probes
specific for each chromosome to differentially label each chromosome.
This technique is more often used in cancer cytogenetics, where complex
chromosome rearrangements can occur.
Array comparative genomic hybridization
is a new molecular technique that involves hybridization of an
individual DNA sample to a glass slide or microarray chip containing
molecular probes (ranging from large ~200kb bacterial artificial chromosomes
to small oligonucleotides) that represent unique regions of the genome.
This method is particularly sensitive for detection of genomic gains
or losses across the genome but does not detect balanced translocations
or distinguish the location of duplicated genetic material (for example,
a tandem duplication versus an insertional duplication).
Basic metabolic studies
Biochemical
studies are performed to screen for imbalances of metabolites in the
bodily fluid, usually the blood (plasma/serum) or urine, but also in
cerebrospinal fluid (CSF). Specific tests of enzyme function (either in
leukocytes, skin fibroblasts, liver, or muscle) are also employed under
certain circumstances. In the US, the newborn screen incorporates biochemical tests to screen for treatable conditions such as galactosemia and phenylketonuria (PKU). Patients suspected to have a metabolic condition might undergo the following tests:
Urine organic acid analysis can be either performed using
quantitative or qualitative methods, but in either case the test is used
to detect the excretion of abnormal organic acids.
These compounds are normally produced during bodily metabolism of
amino acids and odd-chain fatty acids, but accumulate in patients with
certain metabolic conditions.
The acylcarnitine combination profile detects compounds such as
organic acids and fatty acids conjugated to carnitine. The test is used
for detection of disorders involving fatty acid metabolism, including MCAD.
Pyruvate and lactate are byproducts of normal metabolism, particularly during anaerobic metabolism.
These compounds normally accumulate during exercise or ischemia, but
are also elevated in patients with disorders of pyruvate metabolism or
mitochondrial disorders.
Ammonia is an end product of amino acid metabolism and is converted in the liver to urea through a series of enzymatic reactions termed the urea cycle. Elevated ammonia can therefore be detected in patients with urea cycle disorders, as well as other conditions involving liver failure.
Enzyme testing is performed for a wide range of metabolic disorders to confirm a diagnosis suspected based on screening tests.
Molecular studies
DNA sequencing
is used to directly analyze the genomic DNA sequence of a particular
gene. In general, only the parts of the gene that code for the
expressed protein (exons) and small amounts of the flanking untranslated regions and introns
are analyzed. Therefore, although these tests are highly specific and
sensitive, they do not routinely identify all of the mutations that
could cause disease.
Short tandem repeats are unique markers that can be used to determine haplotypes and are used in identity testing for maternal cell contamination.
Treatments
Each cell of the body contains the hereditary information (DNA) wrapped up in structures called chromosomes.
Since genetic syndromes are typically the result of alterations of the
chromosomes or genes, there is no treatment currently available that
can correct the genetic alterations in every cell of the body.
Therefore, there is currently no "cure" for genetic disorders. However,
for many genetic syndromes there is treatment available to manage the
symptoms. In some cases, particularly inborn errors of metabolism,
the mechanism of disease is well understood and offers the potential
for dietary and medical management to prevent or reduce the long-term
complications. In other cases, infusion therapy is used to replace the missing enzyme. Current research is actively seeking to use gene therapy or other new medications to treat specific genetic disorders.
Management of metabolic disorders
In
general, metabolic disorders arise from enzyme deficiencies that
disrupt normal metabolic pathways. For instance, in the hypothetical
example:
A ---> B ---> C ---> D AAAA ---> BBBBBB ---> CCCCCCCCCC ---> (no D)
X Y Z X Y | (no or insufficient Z)
EEEEE
Compound "A" is metabolized to "B" by enzyme "X", compound "B" is
metabolized to "C" by enzyme "Y", and compound "C" is metabolized to "D"
by enzyme "Z".
If enzyme "Z" is missing, compound "D" will be missing, while compounds
"A", "B", and "C" will build up. The pathogenesis of this particular
condition could result from lack of compound "D", if it is critical for
some cellular function, or from toxicity due to excess "A", "B", and/or
"C", or from toxicity due to the excess of "E" which is normally only
present in small amounts and only accumulates when "C" is in excess. Treatment of the metabolic disorder could be achieved through dietary
supplementation of compound "D" and dietary restriction of compounds
"A", "B", and/or "C" or by treatment with a medication that promoted
disposal of excess "A", "B", "C" or "E". Another approach that can be
taken is enzyme replacement therapy, in which a patient is given an
infusion of the missing enzyme "Z" or cofactor therapy to increase the
efficacy of any residual "Z" activity.
Diet
Dietary restriction and supplementation are key measures taken in several well-known metabolic disorders, including galactosemia, phenylketonuria (PKU), maple syrup urine disease, organic acidurias and urea cycle disorders.
Such restrictive diets can be difficult for the patient and family to
maintain, and require close consultation with a nutritionist who has
special experience in metabolic disorders. The composition of the diet
will change depending on the caloric needs of the growing child and
special attention is needed during a pregnancy if a woman is affected
with one of these disorders.
Medication
Medical approaches include enhancement of residual enzyme activity
(in cases where the enzyme is made but is not functioning properly),
inhibition of other enzymes in the biochemical pathway to prevent
buildup of a toxic compound, or diversion of a toxic compound to another
form that can be excreted. Examples include the use of high doses of pyridoxine (vitamin B6) in some patients with homocystinuria to boost the activity of the residual cystathione synthase enzyme, administration of biotin to restore activity of several enzymes affected by deficiency of biotinidase, treatment with NTBC in Tyrosinemia to inhibit the production of succinylacetone which causes liver toxicity, and the use of sodium benzoate to decrease ammonia build-up in urea cycle disorders.
Certain lysosomal storage diseases
are treated with infusions of a recombinant enzyme (produced in a
laboratory), which can reduce the accumulation of the compounds in
various tissues. Examples include Gaucher disease, Fabry disease, Mucopolysaccharidoses and Glycogen storage disease type II. Such treatments are limited by the ability of the enzyme to reach the affected areas (the blood brain barrier
prevents enzyme from reaching the brain, for example), and can
sometimes be associated with allergic reactions. The long-term clinical
effectiveness of enzyme replacement therapies vary widely among
different disorders.
Other examples
Angiotensin receptor blockers in Marfan syndrome & Loeys-Dietz
Bone marrow transplantation
Gene therapy
Career paths and training
Geneticist working with a pedigree
There
are a variety of career paths within the field of medical genetics, and
naturally the training required for each area differs considerably. The
information included in this section applies to the typical pathways in
the United States and there may be differences in other countries. US
practitioners in clinical, counseling, or diagnostic subspecialties
generally obtain board certification through the American Board of Medical Genetics.
A clinical geneticist is typically a physician who evaluates
patients in the office or as a hospital consultation. This process
includes a medical history, family history (pedigree), a detailed physical examination, reviewing objective data such as imaging and test results, establishing a differential diagnosis, and recommending appropriate diagnostic tests.
College (4 yrs) → Medical school (4 yrs) → Primary residency (2-3
yrs) → Residency in Clinical genetics (2 yrs). Some Clinical
geneticists also obtain a PhD degree (4-7 yrs). A new residency track
offers a 4 yr primary residency in Clinical genetics immediately after
finishing Medical school.
Genetic Counselor
MS
A Genetic counselor
specializes in communication of genetic information to patients and
families. Genetic counselors often work closely with Clinical
geneticists or other physicians (such as Obstetricians or Oncologists) and often convey the results of the recommended tests.
College (4 yrs) → Graduate program in Genetic counseling (2 yrs).
Metabolic nurse and/or nutritionist
BA/BS, MS, RN
One of the critical aspects of the management of patients with
metabolic disorders is the appropriate nutritional intervention (either
restricting the compound that cannot be metabolized, or supplementing
compounds that are deficient as the result of an enzyme deficiency).
The metabolic nurse and nutritionist play important roles in
coordinating the dietary management.
College (4 yrs) → Nursing school or graduate training in nutrition.
Individuals who specialize in Biochemical genetics typically work in the diagnostic laboratory, analyzing and interpreting specialized biochemical tests that measure amino acids, organic acids, and enzyme activity. Some Clinical Geneticists are also board certified in Biochemical Genetics.
College (4 yrs) → Graduate school (PhD, usually 4–7 years) and/or Medical school (4 years)
Cytogenetic Diagnostics
BS, MS, PhD, MD, DO, MD-PhD
Individuals who specialize in Cytogenetics typically work in the diagnostic laboratory, analyzing and interpreting karyotypes, FISH, and comparative genomic hybridization tests. Some Clinical Geneticists are also board certified in Cytogenetics.
College (4 yrs) → Graduate school (PhD, usually 4–7 years) and/or Medical school (4 years)
Molecular Genetics
BS, MS, PhD, MD, DO, MD-PhD
Individuals who specialize in Molecular genetics
typically work in the diagnostic laboratory, analyzing and interpreting
specialized genetic tests that look for disease-causing changes (mutations) in the DNA. Some examples of molecular diagnostic tests include DNA sequencing and Southern blotting.
College (4 yrs) → Graduate school (PhD, usually 4–7 years) and/or Medical school (4 years)
Research Geneticist
BS, MS, PhD, MD, DO, MD-PhD
Any researcher who studies the genetic basis of human disease or
uses model organisms to study disease mechanisms could be considered a
Research Geneticist. Many of the clinical career paths also include
basic or translational research, and thus individuals in the field of
medical genetics often participate in some form of research.
College (4 yrs) → Graduate school (PhD, usually 4–7 years) and/or
Medical school (4 years) → Post-doctoral research training (usually 3+
years)
Laboratory Technician
AS, BS, MS
Technicians in the diagnostic or research labs handle samples and run the assays at the bench.
College (4 yrs), may have higher degree (MS, 2+ years)
Ethical, legal and social implications
Genetic
information provides a unique type of knowledge about an individual and
his/her family, fundamentally different from a typically laboratory
test that provides a "snapshot" of an individual's health status. The
unique status of genetic information and inherited disease has a number
of ramifications with regard to ethical, legal, and societal concerns.
On 19 March 2015, scientists urged a worldwide ban on clinical use of methods, particularly the use of CRISPR and zinc finger, to edit the human genome in a way that can be inherited. In April 2015 and April 2016, Chinese researchers reported results of basic research to edit the DNA of non-viable human embryos using CRISPR. In February 2016, British scientists were given permission by regulators to genetically modify human embryos by using CRISPR and related techniques on condition that the embryos were destroyed within seven days.
In June 2016 the Dutch government was reported to be planning to
follow suit with similar regulations which would specify a 14-day limit.
Medical genetics is now recognized as a distinct medical
specialty in the U.S. with its own approved board (the American Board of
Medical Genetics) and clinical specialty college (the American College of Medical Genetics). The College holds an annual scientific meeting, publishes a monthly journal, Genetics in Medicine, and issues position papers and clinical practice guidelines on a variety of topics relevant to human genetics.
Research
The broad range of research in medical genetics reflects the overall
scope of this field, including basic research on genetic inheritance and
the human genome, mechanisms of genetic and metabolic disorders,
translational research on new treatment modalities, and the impact of
genetic testing
Basic genetics research
Basic research geneticists usually undertake research in universities, biotechnology firms and research institutes.
Allelic architecture of disease
Sometimes the link between a disease and an unusual gene variant is
more subtle. The genetic architecture of common diseases is an important
factor in determining the extent to which patterns of genetic variation
influence group differences in health outcomes. According to the common disease/common variant
hypothesis, common variants present in the ancestral population before
the dispersal of modern humans from Africa play an important role in
human diseases.
Genetic variants associated with Alzheimer disease, deep venous
thrombosis, Crohn disease, and type 2 diabetes appear to adhere to this
model. However, the generality of the model has not yet been established and, in some cases, is in doubt. Some diseases, such as many common cancers, appear not to be well described by the common disease/common variant model.
Another possibility is that common diseases arise in part through
the action of combinations of variants that are individually rare.
Most of the disease-associated alleles discovered to date have been
rare, and rare variants are more likely than common variants to be
differentially distributed among groups distinguished by ancestry.
However, groups could harbor different, though perhaps overlapping,
sets of rare variants, which would reduce contrasts between groups in
the incidence of the disease.
The number of variants contributing to a disease and the
interactions among those variants also could influence the distribution
of diseases among groups. The difficulty that has been encountered in
finding contributory alleles for complex diseases and in replicating
positive associations suggests that many complex diseases involve
numerous variants rather than a moderate number of alleles, and the
influence of any given variant may depend in critical ways on the
genetic and environmental background.
If many alleles are required to increase susceptibility to a disease,
the odds are low that the necessary combination of alleles would become
concentrated in a particular group purely through drift.
Population substructure in genetics research
One area in which population categories can be important
considerations in genetics research is in controlling for confounding
between population substructure,
environmental exposures, and health outcomes. Association studies can
produce spurious results if cases and controls have differing allele
frequencies for genes that are not related to the disease being studied, although the magnitude of this problem in genetic association studies is subject to debate. Various methods have been developed to detect and account for population substructure, but these methods can be difficult to apply in practice.
Population substructure also can be used to advantage in genetic
association studies. For example, populations that represent recent
mixtures of geographically separated ancestral groups can exhibit
longer-range linkage disequilibrium between susceptibility alleles and
genetic markers than is the case for other populations.
Genetic studies can use this admixture linkage disequilibrium to search
for disease alleles with fewer markers than would be needed otherwise.
Association studies also can take advantage of the contrasting
experiences of racial or ethnic groups, including migrant groups, to
search for interactions between particular alleles and environmental
factors that might influence health.
Scientific studies have found that numerous brain areas show altered activity in patients suffering from depression,
and this has encouraged advocates of various theories that seek to
identify a biochemical origin of the disease, as opposed to theories
that emphasize psychological or situational causes. Several theories
concerning the biologically based cause of depression have been suggested over the years, including theories revolving around monoamine neurotransmitters, neuroplasticity, inflammation and the circadian rhythm.
Neural circuits
implicated in depression include those involved in the generation and
regulation of emotion, as well as in reward. Abnormalities are commonly
found in the lateral prefrontal cortex whose putative function is
generally considered to involve regulation of emotion. Regions involved
in the generation of emotion and reward such as the amygdala, anterior cingulate cortex (ACC), orbitofrontal cortex (OFC), and striatum
are frequently implicated as well. These regions are innervated by a
monoaminergic nuclei, and tentative evidence suggests a potential role
for abnormal monoaminergic activity.
Genetic factors
Genetic
factors involved in depression have been difficult to identify.
Historically, candidate gene studies have been a major focus of study.
However, as the number of genes reduces the likelihood of choosing a
correct candidate gene, Type I errors (false positives)
are highly likely. Candidate genes studies frequently possess a number
of flaws, including frequent genotyping errors and being statistically
underpowered. These effects are compounded by the usual assessment of
genes without regard for gene-gene interactions. These limitations are
reflected in the fact that no candidate gene has reached genome-wide
significance.
A 2003 study study proposed that a gene-environment interaction
(GxE) may explain why life stress is a predictor for depressive
episodes in some individuals, but not in others, depending on an allelic
variation of the serotonin-transporter-linked promoter region (5-HTTLPR).
As of 2018, five meta analyses of the 5-HTTLPR GxE interaction have
been performed. Two 2009 meta analyses reported null findings, while a 2011 meta analysis with more liberal inclusion criteria reported a significant relaitonship. A 2016 meta analysis concluded that evidence for a GxE interaction was, at best, weak. A 2018 meta analysis reported a weak but significant relationship that was limited by significant heterogeniety.
BDNF
polymorphisms have also been hypothesized to have a genetic influence,
but replication results have been mixed and, as of 2005, were
insufficient for a meta-analysis. Studies also indicate an association of decreased BDNF production with suicidal behavior.
However, findings from gene-environment interactions studies suggest
that the current BDNF models of depression are too simplistic. A 2008 study found interactions (biological epistasis) in the signaling pathways of the BDNF and the serotonin transporter; the BDNF Val66Met
allele, which was predicted to have reduced responsitivity to
serotonin, was found to exercise protective effects in individuals with
the short 5-HTTLPR allele that is otherwise believed to predispose
individuals to depressive episodes after stressful events.
Thus, the BDNF-mediated signalling involved in neuroplastic responses
to stress and antidepressants is influenced by other genetic and
environmental modifiers.
The largest genome meta analysis to date failed to identify
variants with genome-wide significance, with a study size of 18,000
participants of European ancestry.
A 2015 GWAS study in Han Chinese women positively identified two variants in intronic regions near SIRT1 and LHPP with a genome-wide significant association.
Attempts to find a correlation between norepinephrine transporter polymorphisms and depression have yielded negative results.
One review identified multiple frequently studied candidate genes. The genes encoding for the 5-HTT and 5-HT2A receptor were inconsistently associated with depression and treatment response. Mixed results were found for brain-derived neurotrophic factor (BDNF) Val66Met polymorphisms. Polymorphisms in the tryptophan hydroxylase gene was found to be tentatively associated with suicidal behavior.
A meta analysis of 182 case controlled genetic studies published in
2008 found Apolipoprotein verepsilon 2 to be protective, and GNB3 825T,
MTHFR 677T, SLC6A4 44bp insertion or deletions, and SLC6A3 40 bpVNTR
9/10 genotype to confer risk.
Circadian rhythm
Depression may be related to the same brain mechanisms that control the cycles of sleep and wakefulness.
Depression may be related to abnormalities in the circadian rhythm, or biological clock. For example, rapid eye movement (REM) sleep—the stage in which dreaming occurs—may be quick to arrive and intense in depressed people. REM sleep depends on decreased serotonin levels in the brain stem, and is impaired by compounds, such as antidepressants, that increase serotonergic tone in brain stem structures. Overall, the serotonergic system is least active during sleep and most active during wakefulness. Prolonged wakefulness due to sleep deprivation
activates serotonergic neurons, leading to processes similar to the
therapeutic effect of antidepressants, such as the selective serotonin
reuptake inhibitors (SSRIs). Depressed individuals can exhibit a
significant lift in mood after a night of sleep deprivation. SSRIs may
directly depend on the increase of central serotonergic
neurotransmission for their therapeutic effect, the same system that
impacts cycles of sleep and wakefulness.
Research on the effects of light therapy on seasonal affective disorder
suggests that light deprivation is related to decreased activity in the
serotonergic system and to abnormalities in the sleep cycle,
particularly insomnia. Exposure to light also targets the serotonergic
system, providing more support for the important role this system may
play in depression. Sleep deprivation and light therapy
both target the same brain neurotransmitter system and brain areas as
antidepressant drugs, and are now used clinically to treat depression.
Light therapy, sleep deprivation and sleep time displacement (sleep
phase advance therapy) are being used in combination quickly to
interrupt a deep depression in hospitalized patients.
Increased and decreased sleep length appears to be a risk factor for depression.
Patients with MDD sometimes show diurnal and seasonal variation of
symptom severity, even in non-seasonal depression. Diurnal mood
improvement was associated with activity of dorsal neural networks.
Increased mean core temperature was also observed. One hypothesis
proposed that depression was a result of a phase shift.
Daytime light exposure correlates with decreased serotonin
transporter activity, which may underlie the seasonality of some
depression.
Monoamines
Illustration of the major elements in a prototypical synapse. Synapses are gaps between nerve cells. These cells convert their electrical impulses into bursts of chemical relayers, called neurotransmitters, which travel across the synapses to receptors on adjacent cells, triggering electrical impulses to travel down the latter cells.
Monoamines are neurotransmitters that include serotonin, dopamine, norepinephrine, and epinephrine. Many antidepressant drugs acutely increase synaptic
levels of the monoamine neurotransmitter, serotonin, but they may also
enhance the levels of two other neurotransmitters, norepinephrine and
dopamine. The observation of this efficacy led to the monoamine hypothesis of depression,
which postulates that the deficit of certain neurotransmitters is
responsible for depression, and even that certain neurotransmitters are
linked to specific symptoms. The proponents of this hypothesis recommend
choosing the antidepressant with the mechanism of action impacting the
most prominent symptoms. Anxious or irritable patients should be treated
with SSRIs or norepinephrine reuptake inhibitors, and the ones with the loss of energy and enjoyment of life—with norepinephrine and dopamine enhancing drugs.
Others have also proposed the relationship between monoamines and
phenotypes such as serotonin in sleep and suicide, norepinephrine in
dysphoria, fatigue, apathy, cognitive dysfunction, and dopamine in loss
of motivation and psychomotor symptoms.
One explanation for the therapeutic lag is that the initial increase
in synaptic serotonin is only temporary, as firing of serotonergic
neurons in the dorsal raphe adapt via the activity of 5-HT1Aautoreceptors. The therapeutic effect of antidepressants is thought to arise from
autoreceptor desensitization over a period of time, eventually elevating
firing of serotonergic neurons.
Monoamine receptors affect phospholipase C and adenylyl cyclase
inside of the cell. Green arrows means stimulation and red arrows
inhibition. Serotonin receptors are blue, norepinephrine orange, and
dopamine yellow. Phospholipase C and adenylyl cyclase start a signaling cascade
which turn on or off genes in the cell. The 5HT-3 receptor is
associated with gastrointestinal adverse effects and has no relationship
to the other monoamine receptors.
Initial studies of serotonin in depression examined peripheral measures such as the serotonin metabolite 5-Hydroxyindoleacetic acid (5-HIAA)
and platelet binding. The results were generally inconsistent, and may
not generalize to the central nervous system. However evidence from receptor binding studies and pharmacological challenges provide some evidence for dysfunction of serotonin neurotransmission in depression. Serotonin may indirectly influence mood by altering emotional processing biases that are seen at both the cognitive/behavioral and neural level. Pharmacologically reducing serotonin synthesis, and pharmacologically
enhancing synaptic serotonin can produce and attenuate negative
affective biases, respectively. These emotional processing biases may
explain the therapeutic gap.
While various abnormalities have been observed in dopaminergic
systems, results have been inconsistent. Patients with MDD have an
increased reward response to dextroamphetamine
compared to controls, and it has been suggested that this results from
hypersensitivity of dopaminergic pathways due to natural hypoactivity.
While polymorphisms of the D4 and D3 receptor have been implicated in
depression, associations have not been consistently replicated. Similar
inconsistency has been found in postmortem studies, but various
dopamine receptor agonist show promise in treating MDD
There is some evidence that there is decreased nigrostriatal activity
in those with melancholic depression(psychomotor retardation).
Further supporting the role of dopamine in depression is the
consistent finding of decreased cerebrospinal fluid and jugular
metabolites of dopamine, as well as post mortem findings of altered Dopamine receptor D3 and dopamine transporter expression. Studies in rodents have supported a potential mechanism involving stress induced dysfunction of dopaminergic systems.
A number of lines of evidence indicative of decreased adrenergic
activity in depression have been reported. Findings include decreased
activity of tyrosine hydroxylase, decreased size of the locus coeruleus,
increased alpha 2 adrenergic receptor density, and decreased alpha 1
receptor density. Furthermore, norepinephrine transporter knockout in mice models
increase their tolerance to stress, implicating norepinephrine in
depression.
One method used to study the role of monoamines is monoamine depletion. Depletion of tryptophan (the precursor of serotonin), tyrosine and phenylalanine
(precursors to dopamine) does result in decreased mood in those with a
predisposition to depression, but not healthy persons. On the other
hand, inhibition of dopamine and norepinephrine synthesis with alpha-methyl-para-tyrosine does not consistently result in decreased mood.
Monoamine oxidase
An offshoot of the monoamine hypothesis suggests that monoamine oxidase A
(MAO-A), an enzyme which metabolizes monoamines, may be overly active
in depressed people. This would, in turn, cause the lowered levels of
monoamines. This hypothesis received support from a PET study, which found significantly elevated activity of MAO-A in the brain of some depressed people. In genetic studies, the alterations of MAO-A-related genes have not been consistently associated with depression. Contrary to the assumptions of the monoamine hypothesis, lowered but
not heightened activity of MAO-A was associated with the depressive
symptoms in youth. This association was observed only in maltreated
youth, indicating that both biological (MAO genes) and psychological
(maltreatment) factors are important in the development of depressive
disorders.
In addition, some evidence indicates that problems in information
processing within neural networks, rather than changes in chemical
balance, might underlie depression.
Limitations
Since
the 1990s, research has uncovered multiple limitations of the monoamine
hypothesis, and its inadequacy has been criticized within the
psychiatric community. For one thing, serotonin system dysfunction cannot be the sole cause of depression; antidepressants
usually increase synaptic serotonin very quickly, but it often takes at
least two to four weeks before mood improves significantly. One
possible explanation for this lag is that the neurotransmitter activity
enhancement is the result of auto receptor desensitization rather which
can take weeks.
Intensive investigation has failed to find convincing evidence of a
primary dysfunction of a specific monoamine system in patients with major depressive disorders. The antidepressants that do not act through the monoamine system, such as tianeptine and opipramol, have been known for a long time. There has also been inconsistency with regards to serum 5-HIAA levels, a metabolite of serotonin.
Experiments with pharmacological agents that cause depletion of
monoamines have shown that this depletion does not cause depression in
healthy people.
Another problem that presents is that drugs that deplete monoamines
may actually have antidepressants properties. Furthermore, some have
argued that depression may be marked by a hyperserotonergic state Already limited, the monoamine hypothesis has been further oversimplified when presented to the general public.
Receptor binding
As
of 2012, efforts to determine differences in neurotransmitter receptor
expression or for function in the brains of people with MDD using positron emission tomography (PET) had shown inconsistent results. Using the PET imaging technology and reagents available as of 2012, it appeared that the D1 receptor may be underexpressed in the striatum of people with MDD. 5-HT1A receptor binding literature is inconsistent however it leans towards a general decrease in the mesiotemporal cortex. 5-HT2A
receptor binding appears to be unregulated in depressed patients.
Studies on 5-HTT binding are variable but tend towards an increase.
Results with D2/D3 receptor
binding studies are too inconsistent to draw any conclusions. Evidence
supports increase MAO activity in depressed patients, and it may even
be a trait marker (not changed by response to treatment). Muscarinic
receptor binding appears to be increased in depression, and given ligand
binding dynamics, suggests increased cholinergic activity.
Four meta analyses on receptor binding in depression have been performed, two on serotonin transporter (5-HTT), one on 5-HT1A, and another on dopamine transporter (DAT). One meta analysis on 5-HTT reported that binding was reduced in the midbrain and amygdala, with the former correlating with greater age, and the latter correlating with depression severity.
Another meta-analysis on 5-HTT including both post-mortem and in vivo
receptor binding studies reported that while in vivo studies found
reduced 5-HTT in the striatum, amygdala and midbrain, post mortem
studies found no significant associations. 5-HT1A
was found to be reduced in the anterior cingulate cortex, mesiotemporal
lobe, insula, and hippocampus, but not in the amygdala or occipital
lobe. The most commonly used 5-HT1A ligands are not displaced by endogenous serotonin, indicating that receptor density or affinity is reduced. Dopamine transporter binding is not changed in depression.
Emotional processing and neural circuits
Emotional Bias
People with MDD show a number of biases in emotional processing,
such as a tendency to rate happy faces more negatively, and a tendency
to allocate more attentional resources to sad expressions. Depressed people also have impaired recognition of happy, angry, disgusted, fearful and surprised, but not sad faces.
Functional neuroimaging has demonstrated hyperactivity of various brain
regions in response to negative emotional stimuli, and hypoactivity in
response to positive stimuli. One meta analysis reported that depressed
subjects showed decreased activity in the left dorsolateral prefrontal cortex and increased activity in the amygdala in response to negative stimuli.
Another meta analysis reported elevated hippocampus and thalamus
activity in a subgroup of depressed subjects who were medication naive,
not elderly, and had no comorbidities.
The therapeutic lag of antidepressants has been suggested to be a
result of antidepressants modifying emotional processing leading to mood
changes. This is supported by the observation that both acute and
subchronic SSRI administration increases response to positive faces. Antidepressant treatment appears to reverse mood congruent biases in limbic,
prefrontal, and fusiform areas. dlPFC response is enhanced and
amygdala response is attenuated during processing of negative emotions,
the former or which is thought to reflect increased top down regulation.
The fusiform gyrus and other visual processing areas
respond more strongly to positive stimuli with antidepressant
treatment, which is thought to reflect the a positive processing bias.
These effects do not appear to be unique to serotonergic or
noradrenergic antidepressants, but also occur in other forms of
treatment such as deep brain stimulation.
Neural circuits
One
meta analysis of functional neuroimaging in depression observed a
pattern of abnormal neural activity hypothesized to reflect an emotional
processing bias. Relative to controls, depressed patients showed
hyperactivity of circuits in the salience network (SN), composed of the pulvinar nuclei, the insula,
and the dorsal anterior cingulate cortex (dACC), as well as decreased
activity in regulatory circuits composed of the striatum and dlPFC.
Rendition of the Limbic-cortical-striatal-pallidal-thalamic circuit as described by Drevets et al. 2008
A neuroanatomical model called the limbic-cortical model has been
proposed to explain early biological findings in depression. The model
attempts to relate specific symptoms of depression to neurological
abnormalities. Elevated resting amygdala activity was proposed to
underlie rumination, as stimulation of the amygdala has been reported to
be associated with the intrusive recall of negative memories. The ACC
was divided into pregenual (pgACC) and subgenual regions (sgACC),
with the former being electrophysiologically associated with fear, and
the latter being metabolically implicated in sadness in healthy
subjects. Hyperactivity of the lateral orbitofrontal and insular
regions, along with abnormalities in lateral prefrontal regions was
suggested to underlie maladaptive emotional responses, given the regions
roles in reward learning. This model and another termed "the cortical striatal model", which focused more on abnormalities in the cortico-basal ganglia-thalamo-cortical loop,
have been supported by recent literature. Reduced striatal activity,
elevated OFC activity, and elevated sgACC activity were all findings
consistent with the proposed models. However, amygdala activity was
reported to be decreased, contrary to the limbic-cortical model. Furthermore, only lateral prefrontal regions were modulated by
treatment, indicating that prefrontal areas are state markers(i.e.
dependent upon mood), while subcortical abnormalities are trait
markers(i.e. reflect a susceptibility).
Reward
While depression severity as a whole is not correlated with a blunted neural response to reward, anhedonia is directly correlated to reduced activity in the reward system.
The study of reward in depression is limited by heterogeniety in the
definition and conceptualizations of reward and anhedonia. Anhedonia is
broadly defined as a reduced ability to feel pleasure,
but questionnaires and clinical assessments rarely distinguish between
motivational "wanting" and consummatory "liking". While a number of
studies suggest that depressed subjects rate positive stimuli less
positively and as less arousing, a number of studies fail to find a
difference. Furthermore, response to natural rewards such as sucrose does not appear to be attenuated. General affective blunting
may explain "anhedonic" symptoms in depression, as meta analysis of
both positive and negative stimuli reveal reduced rating of intensity.
As anhedonia is a prominent symptom of depression, direct comparison
of depressed with healthy subjects reveals increased activation of the subgenual anterior cingulate cortex (sgACC), and reduced activation of the ventral striatum, and in particular the nucleus accumbens (NAcc) in response to positive stimuli.
Although the finding of reduced NAcc activity during reward paradigms
is fairly consistent, the NAcc is made up of a functionally diverse
range of neurons, and reduced blood-oxygen-level dependent (BOLD) signal in this region could indicate a variety of things including reduced afferent activity or reduced inhibitory output. Nevertheless, these regions are important in reward processing, and dysfunction of them in depression is thought to underlie anhedonia.
Residual anhedonia that is not well targeted by serotonergic
antidepressants is hypothesized to result from inhibition of dopamine
release by activation of 5-HT2C receptors in the striatum. The response to reward in the medial orbitofrontal cortex (OFC)
is attenuated in depression, while lateral OFC response is enhanced to
punishment. The lateral OFC shows sustained response to absence of
reward or punishment, and it is thought to be necessary for modifying
behavior in response to changing contingencies. Hypersensitivity in the
lOFC may lead to depression by producing a similar effect to learned
helplessness in animals.
Elevated response in the sgACC is a consistent finding in
neuroimaging studies using a number of paradigms including reward
related tasks. Treatment is also associated with attenuated activity in the sgACC, and inhibition of neurons in the rodent homologue of the sgACC, the infralimbic cortex (IL), produces an antidepressant effect.
Hyperactivity of the sgACC has been hypothesized to lead to depression
via attenuating the somatic response to reward or positive stimuli. Contrary to studies of functional magnetic resonance imaging
response in the sgACC during tasks, resting metabolism is reduced in
the sgACC. However, this is only apparent when correcting for the
prominent reduction in sgACC volume associated with depression;
structural abnormalities are evident at a cellular level, as
neuropathological studies report reduced sgACC cell markers. The model
of depression proposed from these findings by Drevets et al. suggests
that reduced sgACC activity results in enhanced sympathetic nervous
system activity and blunted HPA axis feedback.
Activity in the sgACC may also not be causal in depression, as the
authors of one review that examined neuroimaging in depressed subjects
during emotional regulation hypothesized that the pattern of elevated
sgACC activity reflected increased need to modulate automatic emotional
responses in depression. More extensive sgACC and general prefrontal
recruitment during positive emotional processing was associated with
blunted subcortical response to positive emotions, and subject
anhedonia. This was interpreted by the authors to reflect a
downregulation of positive emotions by the excessive recruitment of the
prefrontal cortex.
Neuroanatomy
While
a number of neuroimaging findings are consistently reported in people
with major depressive disorder, the heterogeneity of depressed
populations presents difficulties interpreting these findings. For
example, averaging across populations may hide certain subgroup related
findings; while reduced dlPFC activity is reported in depression, a
subgroup may present with elevated dlPFC activity. Averaging may also
yield statistically significant findings, such as reduced hippocampal
volumes, that are actually present in a subgroup of patients.
Due to these issues and others, including the longitudinal consistency
of depression, most neural models are likely inapplicable to all
depression.
Structural neuroimaging
GMV reductions in MDD and BD
Meta analyses performed using seed-based d mapping
have reported grey matter reductions in a number of frontal regions.
One meta analysis of early onset general depression reported grey matter
reductions in the bilateral anterior cingulate cortex (ACC) and dorsomedial prefrontal cortex (dmPFC).
One study in medication free depression found reductions in the left
middle frontal gyrus, right superior frontal gyrus, and left insula, while reporting increases in the thalamus and cuneus.
One meta analysis on first episode depression observed distinct
patterns of grey matter reductions in medication free, and combined
populations; medication free depression was associated with reductions
in the right dorsolateral prefrontal cortex, right amygdala, and right inferior temporal gyrus;
analysis on a combination of medication free and medicated depression
found reductions in the left insula, right supplementary motor area, and
right middle temporal gyrus.
Another study distinguishing medicated and medication free
populations, albeit not restricted to first episode patients, observed
reductions in the combined population in the bilateral superior, right
middle, and left inferior frontal gyrus, along with the bilateral parahippocampus. Increases in thalamic and ACC grey matter was reported in the medication free and medicated populations respectively.
A meta analysis performed using "activation likelihood estimate"
reported reductions in the paracingulate cortex, dACC and amygdala.
Using statistical parametric mapping, one meta analysis
replicated previous findings of reduced grey matter in the ACC, medial
prefrontal cortex, inferior frontal gyrus, hippocampus and thalamus;
however reductions in the OFC and ventromedial prefrontal cortex grey matter were also reported.
Two studies on depression from the ENIGMA consortium have been
published, one on cortical thickness, and the other on subcortical
volume. Reduced cortical thickness was reported in the bilateral OFC,
ACC, insula, middle temporal gyri, fusiform gyri, and posterior
cingulate cortices, while surface area deficits were found in medial
occipital, inferior parietal, orbitofrontal and precentral regions.
Subcortical abnormalities, including reductions in hippocampus and
amygdala volumes, which were especially pronounced in early onset
depression.
MDD is associated with reduced FA in the ALIC and genu/body of the CC
Multiple meta analysis have been performed on studies assessing white matter integrity using fractional anisotropy (FA). Reduced FA has been reported in the corpus callosum (CC) in both first episode medication naive, and general major depressive populations.
The extent of CC reductions differs from study to study. Medication
naive patients have been reported to have reductions only in the body of
the CC and only in the genu of the CC. On the other hand, general MDD samples have been reported to have reductions in the body of the CC, the body and genu of the CC, and only the genu of the CC. Reductions of FA have also been reported in the anterior limb of the internal capsule (ALIC) and superior longitudinal fasciculus.
Functional neuroimaging
Studies
of resting state activity have utilized a number of indicators of
resting state activity, including regional homogeneity (ReHO), amplitude
of low frequency fluctuations (ALFF), fractional amplitude of low
frequency fluctuations (fALFF), arterial spin labeling (ASL), and positron emission tomography measures of regional cerebral blood flow or metabolism.
Studies using ALFF and fALFF have reported elevations in ACC
activity, with the former primarily reporting more ventral findings, and
the latter more dorsal findings.
A conjunction analysis of ALFF and CBF studies converged on the left
insula, with medication naive patients having increased insula activity.
Elevated caudate CBF was also reported
However, another meta analysis found conjoint reduced CBF and ReHO in
the left insula and superior temporal gyrus, but reported elevated
caudate CBF.
A meta analysis combining multiple indicators of resting activity
reported elevated anterior cingulate, striatal, and thalamic activity
and reduced left insula, post-central gyrus and fusiform gyrus activity.
An activation likelihood estimate (ALE) meta analysis of PET/SPECT
resting state studies reported reduced activity in the left insula,
pregenual and dorsal anterior cingulate cortex and elevated activity in
the thalamus, caudate, anterior hippocampus and amygdala.
Compared to the ALE meta analysis of PET/SPECT studies, a study using
multi-kernel density analysis reported hyperactivity only in the pulvinar nuclei of the thalamus.
Brain regions
Research
on the brains of depressed patients usually shows disturbed patterns of
interaction between multiple parts of the brain. Several areas of the
brain are implicated in studies seeking to more fully understand the
biology of depression:
Subgenual cingulate
Studies have shown that Brodmann area 25, also known as subgenual cingulate, is metabolically overactive in treatment-resistant depression. This region is extremely rich in serotonin transporters and is considered as a governor for a vast network involving areas like hypothalamus and brain stem, which influences changes in appetite and sleep; the amygdala and insula, which affect the mood and anxiety; the hippocampus, which plays an important role in memory formation; and some parts of the frontal cortex
responsible for self-esteem. Thus disturbances in this area or a
smaller than normal size of this area contributes to depression. Deep brain stimulation has been targeted to this region in order to reduce its activity in people with treatment resistant depression.
Prefrontal cortex
One review reported hypoactivity in the prefrontal cortex of those with depression compared to controls.
The prefrontal cortex is involved in emotional processing and
regulation, and dysfunction of this process may be involved in the
etiology of depression. One study on antidepressant treatment found an
increase in PFC activity in response to administration of
antidepressants.
One meta analysis published in 2012 found that areas of the prefrontal
cortex were hypoactive in response to negative stimuli in depressed
patients.
One study suggested that areas of the prefrontal cortex are part of a
network of regions including dorsal and pregenual cingulate, bilateral
middle frontal gyrus, insula and superior temporal gyrus that appear to
be hypoactive in depressed patients. However the authors cautioned that
the exclusion criteria, lack of consistency and small samples limit
results.
Amygdala
The amygdala, a structure involved in emotional processing appears to be hyperactive in those with major depressive disorder.
The amygdala in unmedicated depressed persons tended to be smaller
than in those that were medicated, however aggregate data shows no
difference between depressed and healthy persons.
During emotional processing tasks right amygdala is more active than
the left, however there is no differences during cognitive tasks, and at
rest only the left amygdala appears to be more hyperactive. One study, however, found no difference in amygdala activity during emotional processing tasks.
Hippocampus
Atrophy of the hippocampus has been observed during depression, consistent with animal models of stress and neurogenesis.
Stress can cause depression and depression-like symptoms through
monoaminergic changes in several key brain regions as well as
suppression in hippocampal neurogenesis.
This leads to alteration in emotion and cognition related brain regions
as well as HPA axis dysfunction. Through the dysfunction, the effects
of stress can be exacerbated including its effects on 5-HT. Furthermore,
some of these effects are reversed by antidepressant action, which may
act by increasing hippocampal neurogenesis. This leads to a restoration
in HPA activity and stress reactivity, thus restoring the deleterious
effects induced by stress on 5-HT.
The hypothalamic-pituitary-adrenal axis is a chain of endocrine
structures that are activated during the body's response to stressors
of various sorts. The HPA axis involves three structure, the
hypothalamus which release CRH that stimulates the pituitary gland to release ACTH
which stimulates the adrenal glands to release cortisol. Cortisol has a
negative feedback effect on the pituitary gland and hypothalamus. In
depressed patients the often shows increased activation in depressed
people, but the mechanism behind this is not yet known.
Increased basal cortisol levels and abnormal response to dexamethasone
challenges have been observed in patients with depression. Early life stress has been hypothesized as a potential cause of HPA dysfunction.
HPA axis regulation may be examined through a dexamethasone
suppression tests, which tests the feedback mechanisms. Non-suppression
of dexamethasone is a common finding in depression, but is not
consistent enough to be used as a diagnostic tool.
HPA axis changes by be responsible for some of the changes such as
decreased bone mineral density and increased weight found in patients
with MDD. One drug, ketoconazole, currently under development has shown
promise in treating MDD.
Animal Models
A
number of animal models exist for depression, but they are limited in
that depression involves primarily subjective emotional changes.
However, some of these changes are reflected in physiology and behavior,
the latter of which is the target of many animal models. These models
are generally assessed according to four facets of validity; the
reflection of the core symptoms in the model; the predictive validity of
the model; the validity of the model with regard to human
characteristics of etiology; and the biological plausibility.
Different models for inducing depressive behaviors have been
utilized; neuroanatomical manipulations such as olfactory bulbectomy or
circuit specific manipulations with optogenetics; genetic models such as
5-HT1A knockout or selectively bred animals;
models involving environmental manipulation associated with depression
in humans, including chronic mild stress, early life stress and learned
helplessness.
The validity of these models in producing depressive behaviors may be
assessed with a number of behavioral tests. Anhedonia and motivational
deficits may, for example, be assessed via examining an animals level of
engagement with rewarding stimuli such as sucrose or intracranial
self-stimulation. Anxious and irritable symptoms may be assessed with
exploratory behavior in the presence of a stressful or novelty
environment, such as the open field test, novelty suppressed feeding, or
the elevated plus maze. Fatigue, psychomotor poverty, and agitation
may be assessed with locomotor activity, grooming activity, and open
field tests.
Animal models possess a number of limitations due to the nature
of depression. Some core symptoms of depression, such as rumination,
low self-esteem, guilt, and depressed mood cannot be assessed in animals
as they require subjective reporting.
From an evolutionary standpoint, the behavior correlates of defeats of
loss are thought to be an adaptive response to prevent further loss.
Therefore, attempts to model depression that seek to induce defeat or
despair may actually reflect adaption and not disease. Furthermore,
while depression and anxiety are frequently comorbid, dissociation of
the two in animal models is difficult to achieve.
Pharmacological assessment of validity is frequently disconnected from
clinical pharmacotherapeutics in that most screening tests assess acute
effects, while antidepressants normally take a few weeks to work in
humans.
Neurocircuits
Regions
involved in reward are common targets of manipulation in animal models
of depression, including the nucleus accumbens (NAc), ventral tegmental area (VTA), ventral pallidum (VP), lateral habenula (LHb) and medial prefrontal cortex (mPFC). Tentative fMRI studies in humans demonstrate elevated LHb activity in depression.
The lateral habenula projects to the RMTg to drive inhibition of
dopamine neurons in the VTA during omission of reward. In animal models
of depression, elevated activity has been reported in LHb neurons that
project to the ventral tegmental area (ostensibly
reducing dopamine release). The LHb also projects to aversion reactive
mPFC neurons, which may provide an indirect mechanism for producing
depressive behaviors.
Learned helplessness induced potentiation of LHb synapses are reversed
by antidepressant treatment, providing predictive validity. A number of inputs to the LHb have been implicated in producing
depressive behaviors. Silencing GABAergic projections from the NAc to
the LHb reduces conditioned place preference induced in social
aggression, and activation of these terminals induces CPP. Ventral
pallidum firing is also elevated by stress induced depression, an effect
that is pharmacologically valid, and silencing of these neurons
alleviates behavioral correlates of depression. Tentative in vivo evidence from patients with major depression suggests abnormalities in dopamine signalling.
This led to early studies investigating VTA activity and manipulations
in animal models of depression. Massive destruction of VTA neurons
enhances depressive behaviors, while VTA neurons reduce firing in
response to chronic stress. However, more recent specific manipulations
of the VTA produce varying results, with the specific animal model,
duration of VTA manipulation, method of VTA manipulation, and subregion
of VTA manipulation all potentially leading to differential outcomes.
Stress and social defeat induced depressive symptoms, including
anhedonia, are associated with potentiation of excitatory inputs to Dopamine D2 receptor expressing medium spiny neurons (D2-MSNs)
and depression of excitatory inputs to Dopamine D1 receptor expressing
medium spiny neurons (D1-MSNs). Optogenetic excitation of D1-MSNs
alleviates depressive symptoms and is rewarding, while the same with
D2-MSNs enhances depressive symptoms. Excitation of glutaminergic
inputs from the ventral hippocampus reduces social interactions, and
enhancing these projections produces susceptibility to stress induced
depression.
Manipulations of different regions of the mPFC can produce and
attenuate depressive behaviors. For example, inhibiting mPFC neurons
specifically in the intralimbic cortex attenuates depressive behaviors.
The conflicting findings associated with mPFC stimulation, when
compared to the relatively specific findings in the infralimbic cortex,
suggest that the prelimbic cortex and infralimbic cortex may mediate
opposing effects.
mPFC projections to the raphe nuclei are largely GABAergic, and
inhibit the firing of serotonergic neurons. Specific activation of
these regions reduce immobility in the forced swim test, but do not
affect open field or forced swim behavior. Inhibition of the raphe
shifts the behavioral phenotype of uncontrolled stress to a phenotype
closer to that of controlled stress.
Altered neuroplasticity
Recent studies have called attention to the role of altered neuroplasticity in depression. A review found convergence of three phenomena:
Chronic stress reduces synaptic and dendritic plasticity
Depressed subjects show evidence of impaired neuroplasticity (e.g. shortening and reduced complexity of dendritic trees)
Anti-depressant medications may enhance neuroplasticity at both a molecular and dendritic level.
The conclusion is that disrupted neuroplasticity is an underlying feature of depression, and is reversed by antidepressants.
Blood levels of BDNF in depressed patients increase significantly
with antidepressant treatment and correlate with decrease in symptoms.
Post mortem studies and rat models demonstrate decreased neuronal
density in the prefrontal cortex thickness in depressed patients. Rat
models demonstrate histological changes consistent with MRI findings in
humans, however studies on neurogenesis in humans are limited.
Antidepressants appear to reverse the changes in neurogenesis in both
animal models and humans.
Inflammation and oxidative stress
Various review have found that general inflammation may play a role in depression. One meta analysis of cytokines in depressed patients found increased IL-6 and TNF-a levels relative to controls. First theories came about when it was noticed that interferon therapy caused depression in a large number of patients. Meta analysis on cytokine levels in depressed patients have demonstrated increased levels of IL-1, IL-6, C-reactive protein, but not IL-10 in depressed patients. Increased numbers of T-Cells presenting activation markers, levels of neopterin, IFN gamma, sTNFR, and IL-2 receptors have been observed in depression.
Various sources of inflammation in depressive illness have been
hypothesized and include trauma, sleep problems, diet, smoking and
obesity.
Cytokines, by manipulating neurotransmitters, are involved in the
generation of sickness behavior, which shares some overlap with the
symptoms of depression. Neurotransmitters hypothesized to be affected
include dopamine and serotonin, which are common targets for
antidepressant drugs. Induction of indolamine-2,3 dioxygenease by
cytokines has been proposed as a mechanism by which immune dysfunction
causes depression. One review found normalization of cytokine levels after successful treatment of depression.
A meta analysis published in 2014 found the use of anti-inflammatory
drugs such as NSAIDs and investigational cytokine inhibitors reduced
depressive symptoms.
Inflammation is also intimately linked with metabolic processes
in humans. For example, low levels of Vitamin D have been associated
with greater risk for depression.
The role of metabolic biomarkers in depression is an active research
area. Recent work has explored the potential relationship between plasma
sterols and depressive symptom severity.
Increased markers of oxidative stress relative to controls have been found in patients with MDD. A marker of DNA oxidation, 8-Oxo-2'-deoxyguanosine, has been found to be increased in both the plasma and urine of depressed patients. This along with the finding of increased F2-isoprostanes
levels found in blood, urine and cerebrospinal fluid indicate increased
damage to lipids and DNA in depressed patients. Studies with 8-Oxo-2'
Deoxyguanosine varied by methods of measurement and type of depression,
but F2-Isoprostane level was consistent across depression types.
Authors suggested lifestyle factors, dysregulation of the HPA axis,
immune system and autonomics nervous system as possible causes. Another meta-analysis found similar results with regards to oxidative damage products as well as decreased oxidative capacity.
Large-scale brain network theory
Instead of studying one brain region, studying large scale brain networks is another approach to understanding psychiatric and neurological disorders,
supported by recent research that has shown that multiple brain regions
are involved in these disorders. Understanding the disruptions in these
networks may provide important insights into interventions for treating
these disorders. Recent work suggests that at least three large-scale
brain networks are important in psychopathology:
Central executive network
The executive network is made up of fronto-parietal regions, including dorsolateral prefrontal cortex and lateral posterior parietal cortex. This network is involved in high level cognitive functions such as maintaining and using information in working memory, problem solving, and decision making. Deficiencies in this network are common in most major psychiatric and neurological disorders, including depression.
Because this network is crucial for everyday life activities, those who
are depressed can show impairment in basic activities like test taking
and being decisive.
Default mode network
The default mode network
includes hubs in the prefrontal cortex and posterior cingulate, with
other prominent regions of the network in the medial temporal lobe and
angular gyrus.
The default mode network is usually active during mind-wandering and
thinking about social situations. In contrast, during specific tasks
probed in cognitive science (for example, simple attention tasks), the
default network is often deactivated.
Research has shown that regions in the default mode network (including
medial prefrontal cortex and posterior cingulate) show greater activity
when depressed participants ruminate (that is, when they engage in
repetitive self-focused thinking) than when typical, healthy
participants ruminate.
Individuals suffering from major depression also show increased
connectivity between the default mode network and the subgenual
cingulate and the adjoining ventromedial prefrontal cortex in comparison
to healthy individuals, individuals with dementia or with autism. Numerous studies suggest that the subgenual cingulate plays an important
role in the dysfunction that characterizes major depression.
The increased activation in the default mode network during rumination
and the atypical connectivity between core default mode regions and the
subgenual cingulate may underlie the tendency for depressed individual
to get “stuck” in the negative, self-focused thoughts that often
characterize depression.
However, further research is needed to gain a precise understanding of
how these network interactions map to specific symptoms of depression.
Salience network
The salience network is a cingulate-frontal operculum network that includes core nodes in the anterior cingulate and anterior insula. A salience
network is a large-scale brain network involved in detecting and
orienting the most pertinent of the external stimuli and internal events
being presented. Individuals who have a tendency to experience negative emotional states (scoring high on measures of neuroticism) show an increase in the right anterior insula during decision-making, even if the decision has already been made.
This atypically high activity in the right anterior insula is thought
to contribute to the experience of negative and worrisome feelings. In major depressive disorder, anxiety is often a part of the emotional state that characterizes depression.
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