تسلسل الجينوم الكامل

(تم التحويل من Whole genome sequencing)

تسلسل الجينوم الكامل Whole genome sequencing، هو 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.[2]

Electropherograms are commonly used to sequence portions of genomes.[1]
An image of the 46 chromosomes, making up the diploid genome of human male. (The mitochondrial chromosome is not shown.)

Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014.[3][4][5] In the future of personalized medicine, whole genome sequence data may be an important tool to guide therapeutic intervention.[6] 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.[7] In addition, whole genome sequencing should not be confused with methods that sequence specific subsets of the genome - such methods include whole exome sequencing (1-2% of the genome) or SNP genotyping (<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.[8]

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المصطلح

It is also known as WGS, full genome sequencing, complete genome sequencing, or entire genome sequencing.


التاريخ

 
The first whole genome to be sequenced was of the bacterium Haemophilus influenzae.
 
The worm Caenorhabditis elegans was the first animal to have its whole genome sequenced.
 
Drosophila melanogaster's whole genome was sequenced in 2000.
 
Arabidopsis thaliana was the first plant genome 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.[9]

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.[10]

The first organism to have its entire genome sequenced was Haemophilus influenzae in 1995.[11] 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.[11] In contrast, eukaryotes, both unicellular and multicellular such as Amoeba dubia and humans (Homo sapiens) respectively, have much larger genomes (see C-value paradox).[12] Amoeba dubia has a genome of 700 billion nucleotide pairs spread across thousands of chromosomes.[13] 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.[14]

The first bacterial and archaeal genomes, including that of H. influenzae, were sequenced by Shotgun sequencing.[11] 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,[15] 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.[16] 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).[17]

In 1999, the entire DNA sequence of human chromosome 22, the shortest human autosome, was published.[18] 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.[19] The first plant genome - that of the model organism Arabidopsis thaliana - was also fully sequenced by 2000.[20] By 2001, a draft of the entire human genome sequence was published.[21] The genome of the laboratory mouse Mus musculus was completed in 2002.[22]

In 2004, the Human Genome Project published an incomplete version of the human genome.[23] In 2008, a group from Leiden, The Netherlands, reported the sequencing of the first female human genome (Marjolein Kriek).

Currently thousands of genomes have been wholly or partially sequenced.

التفاصيل التجريبية

استخدام الخلايا للتسلسل

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.[24]

Single cell genome sequencing is being tested as a method of preimplantation genetic diagnosis, wherein a cell from the embryo created by in vitro fertilization is taken and analyzed before embryo transfer into the uterus.[25] After implantation, cell-free fetal DNA can be taken by simple venipuncture from the mother and used for whole genome sequencing of the fetus.[26]

التقنيات المبكرة

 
An ABI PRISM 3100 Genetic Analyzer. Such capillary sequencers automated the early efforts of sequencing genomes.


التقنيات الحالية

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.[27] 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.[28]

التحليل

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.[29]

تجارياً

 
Total cost of sequencing a whole human genome as calculated by the NHGRI.



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مقارنة بتقنيات أخرى

مصفوفات الدنا المكروية

التطبيقات

تسلسلات الطفرات

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.[30][31] 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.[32] 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).[33]

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.[بحاجة لمصدر] 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).[34] Since the haploid human genome consists of approximately 3,200 megabases,[35] 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,[36] such that the gene-rich, early-replicating regions receive fewer mutations than gene-poor, late-replicating heterochromatin, likely due to differential DNA repair activity.[37] In particular, the histone modification H3K9me3 is associated with high,[38] and H3K36me3 with low mutation frequencies.[39]

الدرسات المرتبطة بالجينوم

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.[40]

الاستخدام التشخيصي

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.[41] 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.[41] 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.[41][42][43]

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.[44][45] 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.[46] 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.

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.قالب:Mcn

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.[47] 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.[48][49]

In 2018, researchers at Rady Children's Institute for Genomic Medicine in San Diego, CA determined that rapid whole-genome sequencing (rWGS) can diagnose genetic disorders in time to change acute medical or surgical management (clinical utility) and improve outcomes in acutely ill infants. The researchers reported a retrospective cohort study of acutely ill inpatient infants in a regional children's hospital from July 2016-March 2017. Forty-two families received rWGS for etiologic diagnosis of genetic disorders. The diagnostic sensitivity of rWGS was 43% (eighteen of 42 infants) and 10% (four of 42 infants) for standard genetic tests (P = .0005). The rate of clinical utility of rWGS (31%, thirteen of 42 infants) was significantly greater than for standard genetic tests (2%, one of 42; P = .0015). Eleven (26%) infants with diagnostic rWGS avoided morbidity, one had a 43% reduction in likelihood of mortality, and one started palliative care. In six of the eleven infants, the changes in management reduced inpatient cost by $800,000-$2,000,000. These findings replicate a prior study of the clinical utility of rWGS in acutely ill inpatient infants, and demonstrate improved outcomes and net healthcare savings. rWGS merits consideration as a first tier test in this setting.[50]

الاعتبارات الأخلاقية

أشخاص ذوي تسلسل جينومي شائع

انظر أيضاً

المصادر

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وصلات خارجية

قالب:Emerging biomedical technologies