Nclinical whole-exome sequencing for the diagnosis of mendelian disorders pdf

Nicolae,4 and xihong lin5 many sequencing studies are now underway to identify the genetic causes for both mendelian and complex traits. In conclusion, the use of wholeexome sequencing to analyze 250 consecutive clinical cases yielded a diagnosis in 25% of these cases, which supports the use of wholeexome sequencing as a diagnostic test for patients with nonspecific or unusual disease presentations of possible genetic cause and for patients with clinical diagnoses of heterogeneous genetic conditions. Family relationships could be inaccurate, to put it politely. Genome sequencing and implications for rare disorders orphanet. Jun 16, 2015 clinical exome sequencing ces has become an increasingly popular diagnostic tool in patients with heterogeneous genetic disorders, especially in those with neurocognitive phenotypes. Whole exome sequencing wes is utilized for the clinical care of children with mendelian disorders and cancer. Solving the molecular diagnostic testing conundrum for. Implementing clinical whole exome sequencing for the care. Based upon published reports, a diagnosis is identified in triobased whole exome sequencing in approximately 25% to 37% of cases. Oct 17, 20 whole exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders.

Exome sequencing, also known as whole exome sequencing wes, is a genomic technique for sequencing all of the proteincoding regions of genes in a genome known as the exome. Consistent with these data, the pace of novel disease gene discovery does. Ngs allows for the analysis of multiple regions of the genome in one single reaction and has been shown to be a costeffective and efficient tool in investigating patients with mendelian diseases. Nextgeneration sequencing in the clinical setting targeted vs whole exome sequencing. Linkage analysis successfully resolved most of the more common singlegene disorders, but until the development of whole genome sequencing, no good alternative approaches were available for conditions that were not. Original article from the new england journal of medicine clinical wholeexome sequencing for the diagnosis of mendelian disorders. Multiphasic analysis of whole exome sequencing data. The patients biological parents must be available and able to provide a blood sample, which is used for comparison purposes. Clinical wholeexome sequencing for the diagnosis of mendelian. Clinical application of wholeexome sequencing across clinical indications. Wholeexome sequencing reanalysis at 12 months boosts diagnosis and is costeffective when applied early in mendelian disorders skip to main content thank you for visiting. Next generation sequencing methods for diagnosis of.

Rare diseases are usually chronically debilitating or even lifethreatening with diagnostic and therapeutic challenges in current clinical practice. Germline disorders, gene rearrangement detection by whole genome nextgeneration. Background wholeexome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders. Clinical exome sequencing for genetic identification of. Clinical exome sequencing for genetic identification of rare mendelian disorders article pdf available in jama the journal of the american medical association 31218 october 2014. We used whole exome data for two mendelian disorders for which the causal gene is known. A previously described 1 wholeexome sequencing protocol, including library construction, exome capture by vcrome version 2. Solving the molecular diagnostic testing conundrum for mendelian disorders in the era of nextgeneration sequencing. Our knowledge of the diversity of mendelian phenotypes is increasingly sophisticated, but substantial gaps remain.

Using wes testing methods, researchers at the baylor college of medicine in houston, texas, were able to diagnose 25% of 250 previously undiagnosed patients with suspected genetic disorders. Mar 18, 20 exome sequencing provides a particularly powerful method with which to identify diseasecausing single nucleotide variations snvs in mendelian disorders 14. We developed technical, bioinformatic, interpretive, and validation pipelines for wholeexome sequencing in a certified clinical laboratory to identify sequence variants underlying disease phenotypes in patients. Oct 17, 20 recurrent clinical phenotypes occurred in patients with mutations that were highly likely to be causative in the same genes and in different genes responsible for genetically heterogeneous disorders. Unlike traditional linkage methods, the underlying gene could be identi ed directly, and by using unrelated subjects.

There are several examples in which the underlying genetic cause was not evident from the phenotype, yet whole exome sequencing revealed mutations in a known disease gene. Dna enrichment and nextgeneration sequencing technology have made it possible to quickly and costeffectively sequence all the genes in the exome, the proteincoding portion of the genome, and then to rapidly identify alleles responsible for mendelian disorders. Of note, the presence of two or more causal genes for different mendelian disorders has been. For example, one patient patient 14 in table s3 in the supplementary appendix had wholeexome sequencing. Recurrent clinical phenotypes occurred in patients with mutations that were highly likely to be causative in the same genes and in different genes responsible for genetically heterogeneous disorders.

Over the past 2 years, experimental and analytical approaches relating to exome sequencing have established a rich framework for discovering the genes underlying unsolved mendelian disorders. May 28, 20 we tested the ability of an aggregate vest gene score to identify candidate mendelian disease genes, based on whole exome sequencing of a small number of disease cases. Linkage studies have previously been the main tool to elucidate the genetics of. Here, dna samples from 106 patients with a clinical suspicion of pid were subjected to wes in order to test the diagnostic yield of this test in a highly consanguineous community. Genetic diagnosis of mendelian disorders via rna sequencing. I tried it on the na19240 hapmap sample from paper below table 3 which shows 196 variants snps and indels. Implementing clinical whole exome sequencing for the care of. Nextgeneration sequencing ngs was developed more than a decade ago to facilitate sequencing of large amounts of genomic data. Clinical application of wholeexome sequencing across. Use of ngs in clinical diagnosis is now widely accepted, with varying roles from gene panel or targeted sequencing, through whole exome sequencing also termed clinical exome sequencing, to whole genome sequencing.

Clinical exome sequencing ces has become an increasingly popular diagnostic tool in patients with heterogeneous genetic disorders, especially in those with neurocognitive phenotypes. A clinical cohort of 149 probands from qatar with suspected mendelian, mainly neurocognitive phenotypes, underwent ces. Overall, among patients who had nonsyndromic disorders with a neurologic phenotype intellectual disability or developmental delay, the diagnostic rate was 33%. Clinical impact and costeffectiveness of whole exome sequencing as a diagnostic tool. Between 2010 and 2015, about 555 genes implicated in mendelian phenotypes were discovered using ngs. This was a wellwritten paper that showcased some of the advantages to whole genome sequencing over exome sequencing for uncovering the genetic basis of rare diseases. This assay, which we term the mendeliome, comprises gene panels based on clinical. Though whole exome sequencing wes has been used to successfully discover many genes that cause mendelian disorders, analysis of wes data remains challenging. However, the exception is inborn errors of metabolism, since many of these disorders. High diagnostic yield of clinical exome sequencing in. Yang et al conducted a singlecenter observational study of 2000 patients with clinical wholeexome sequencing performed for a suspected genetic disorder. Whole exome sequencing wes is proven and medically necessary for the. To understand the contribution of mendelian mutations to the burden of undiagnosed diseases that are suspected to be genetic in origin, we developed a nextgeneration sequencing based multiplexing assay that encompasses the 3000 known mendelian genes. Next generation mendelian genetics by exome sequencing.

Plon, md, phd, facmg departments of pediatricshematologyoncology and molecular and human genetics human genome sequencing center baylor college of. Jun 12, 2017 across a variety of mendelian disorders. Pdf clinical impact and costeffectiveness of whole. Most diagnoses altered the management of infants in the nicu or picu. Jan 12, 2017 this is a clever strategy for beginning to tease out regulatory variation in mendelian disorders, and may help open the door for even more discoveries. Background whole exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders. Application of wes in the clinic to explain the etiology of suspected mendelian disorders has been relatively successful. Whole exome sequencing and homozygosity mapping identify.

Exome sequencing, which sequences the proteincoding region of the genome, has been rapidly applied to variant discovery in research settings and recent increases in accuracy have enabled development of clinical exome sequencing ces for mutation identification in patients with suspected genetic diseases. Implementing clinical whole exome sequencing for the care of children with mendelian disorders and cancer human genome sequencing center national institute of general medical sciences sharon e. Phenotypedriven strategies for exome prioritization of human. Pdf clinical wholeexome sequencing for the diagnosis of. A total of 4 probands received two nonoverlapping molecular diagnoses, which potentially challenged the clinical diagnosis that had been made on the basis of history and physical examination. Her electroretinogram showed diffuse rodcone dysfunction performed at age 39 and visual fields showed a ring scotoma with intact central fields, consistent with a diagnosis of rp data not shown. Sep 27, 2011 exome sequencing is a powerful approach for accelerating the discovery of the genes underlying mendelian disorders and, increasingly, of genes underlying complex traits. Wholegenome sequencing and newer, better algorithms will eventually be required to find the genetic basis of many even mendelian diseases. Identifying mendelian disease genes with the variant effect. Automated pipeline for whole exome genome sequencing analysis on mendelian diseases yunfei guo1,2, gholson j. Unlocking mendelian disease using exome sequencing genome.

Methods and applications iuliana ionitalaza,1, vlad makarov, 2seungtai yoon,2 benjamin raby,3 joseph buxbaum, dan l. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders. Hundreds of novel diseaseassociated genes have been characterized by whole exome sequencing in the past five years, yet the identification of diseasecausing mutations is often challenging because of the large number of rare variants that are being revealed. Clinical exome sequencing detects diseasecausing glitches. Exome or wholegenome sequencing for mendelian disorders. In selected acutely ill infants, statseq had a high rate of diagnosis of genetic disorders. Caperton braxton and joke beuten and fan xia and zhiyv niu.

Jun 26, 2015 while sequencing of the entire genome represents the most comprehensive option, sequencing of its 2 % coding part whole exome sequencing wes has emerged as a cheaper and more practical alternative. Comprehensive gene panels provide advantages over clinical. In 504 cases 25%, the researchers detected variants in known diseasecausing genes that appeared to be aligned with the patients symptoms. The recent use of wholegenome sequencing wgs and wholeexome sequencing wes for diagnosing genetic disease prompted stephen kingsmore at rady childrens. Diagnostic and clinical utility of whole genome sequencing in a. Whole exome and whole genome sequencing page 4 of 24 unitedhealthcare oxford clinical policy effective 09012019 19962019, oxford health plans, llc clinical evidence whole exome sequencing pediatric noncancer the babyseq project is a pilot randomized trial within the newborn sequencing. Wholeexome sequencing provided a diagnosis in 31% of persons with a specific neurologic finding, such as a movement disorder. Ultimately, exome sequencing itself may be the root of many negative results. Revisiting mendelian disorders through exome sequencing. One study evaluated 2,000 people who were referred by physicians to the baylor college of medicine for clinical wholeexome sequencing. Exome sequencing has now become technically feasible and more costeffective due to the recent advances in highthroughput sequence capture methods and nextgeneration sequencing technologies which have offered new opportunities for mendelian disorder research. In 4 unrelated patients with primrose syndrome, including the patients reported by mathijssen et al. Sequencing of the genome or exome for clinical applications, hereafter referred to as.

Original article from the new england journal of medicine clinical diagnosis by wholegenome sequencing of a prenatal sample. This article describes new software called mendel,md, which combines multiple types of filter options and makes use of regularly. Hey all, i only used so far three filters for my whole exome pipeline aligning to hg19 for a hapmap sample. Lyon 3, kai wang1,2,4 1 zilkha neurogenetic institute, 2 department of preventive medicine, 4 department of psychiatry, keck school of medicine. Whole exome sequencing enables scanning a large number of genes for relatively low costs. Jul 17, 2012 the diagnosis could be incorrect for either cases or controls. Wholeexome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders.

High diagnostic yield of clinical exome sequencing in middle. We previously reported methods for diagnosing genetic disorders with rapid wholegenome sequencing statseq in 50 h. One of the biggest challenges clinicians are facing is deciding between using targeted versus whole exome sequencing. Flags, frequently mutated genes in public exomes bmc. More than 180 novel rarediseasecausing genes with mendelian inheritance patterns have been discovered through sequencing the exomes of just a few unrelated individuals or family members. Can exome sequencing be applied to identify the cause of a mendelian disorder. Despite the revolutionizing impact of wholeexome sequencing wes on the molecular genetics of mendelian disorders. In the majority of fetuses with structural malformations, the underlying cause of the anomaly remains unknown.

There are several examples in which the underlying genetic cause was not evident from the phenotype, yet whole exome sequencing. Applications to clinical practice of whole exome sequencing wes and whole genome sequencing wgs technologies and the computational interpretation of rare variants in genome data have been revolutionary, allowing conclusions to diagnostic odysseys and enabling molecular diagnoses for thousands of patients 1,2,3,4,5,6,7. Automated pipeline for whole exomegenome sequencing analysis. Finding disease variants in mendelian disorders by using sequence data. Utility of whole exome sequencing for genetic diagnosis. This led us to suspect that maybe part of the phenotype is caused by these missense variants. Clinical exome sequencing has rapidly become a component of the clinical approach to individuals with rare diseases and is being applied to a wide range of clinical presentations that require a broad search for causal variants across the spectrum of genetically heterogeneous mendelian disorders. Molecular genetic approaches have evolved at astonishing pace in capacity, capability, and application in recent years, reflected by the increasingly routine use of whole exome sequencing wes in mendelian and rare disorder diagnosis. Whole exome sequencing as a diagnostic adjunct to clinical. Over the past several years, more focus has been placed on dissecting the genetic basis of complex diseases and traits through genomewide association studies. The most common cause of mendelian disease is a nonsynonymous singlenucleotide variant nssnv that results in a single amino acid change in the encoded protein 2. Whole exome sequencing identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible. Before ordering wholeexome sequencing, physicians had carried out extensive clinical diagnostic workups, some of which exceeded the time and cost of the clinical wholeexome sequencing. Clinical diagnosis of mendelian disorders using a comprehensive.

Clinical whole exome sequencing for the diagnosis of mendelian disorders. Translation into diseasemodifying treatments is challenging, particularly for intellectual developmental disorder. Wholeexome sequencing wes has been used increasingly in clinical. This results in improved clinical diagnosis, more accurate genotypephenotype correlations and new insights into the role of rare genomic. Clinical exome sequencing targets approximately 22,000. We developed technical, bioinformatic, interpretive, and validation pipelines for whole exome sequencing in a certified. Clinical exome sequencing targets approximately 22,000 proteincoding. Dramatic improvements in dna sequencing technologies and computational analyses have led to wide use of whole exome sequencing wes to identify the genetic basis of mendelian disorders. Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human mendelian disorders. Over the past decade, nextgeneration sequencing ngs has led to an exponential increase in our understanding of the genetic basis of mendelian diseases. In this study, wholeexome sequencing was used as the basis for providing a diagnosis in 47 probands with intellectual developmental disorder and unexplained metabolic phenotypes. Pdf clinical exome sequencing for genetic identification. Whole exome and whole genome sequencing for diagnosis. Wholegenome sequencing for identification of mendelian.

Next generation sequencing in clinical diagnosis the. Clinical wholeexome sequencing for the diagnosis of rare disorders. Although the patients main clinical diagnosis is not mas, her phenotype resembles the ones described in sienis work. Wholeexome sequencing has transformed gene discovery and diagnosis in rare diseases. The clinical application of rna sequencing in genetic. Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits. Sanger sequencing confirmed the presence of dhodh mutations in three additional families with miller syndrome. A clinical cohort of 149 probands from qatar with suspected mendelian. Whole exome sequencing wes approach for diagnosing. Exome sequencing and the management of neurometabolic.

Methods we developed technical, bioinformatic, interpretive, and validation pipelines for wholeexome sequencing in a certified clinical laboratory to identify sequence variants. Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified. Metaanalysis of the diagnostic and clinical utility of. Lessons learned from additional research analyses of unsolved. Pdf high diagnostic yield of clinical exome sequencing. Clinical wholeexome sequencing for the diagnosis of mendelian disorders article pdf available in new england journal of medicine 36916 october 20 with 501 reads how we measure reads. Pdf exome sequencing as a tool for mendelian disease gene. Clinical wholeexome sequencing for the diagnosis of mendelian disorders. Mendelian disorder definition of mendelian disorder by the. A likely genetic diagnosis was achieved in 70% of patients. Pdf background wholeexome sequencing is a diagnostic. Finding genes in mendelian disorders using sequence data. In contrast, mendelian disorders have received little attention mainly due to the lack of newer and more powerful methods to study these disorders. Clinical application of nextgeneration sequencing for.

High diagnostic yield of clinical exome sequencing in middle eastern patients with mendelian disorders article pdf available in human genetics 49 june 2015 with 535 reads. The genetic causes of these diseases can be identified using whole exome sequencing wes. With decreasing sequencing costs, exome sequencing is becoming a standard tool for mapping causal genes for human mendelian diseases. Plon, md, phd, facmg departments of pediatricshematologyoncology and molecular and human genetics human genome sequencing. Exome sequencing as a tool for mendelian disease gene discovery. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods.

Genetic diagnosis of autoinflammatory disease patients. Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. There is a clinical diagnosis of a genetic condition that can be. Clinical wholeexome sequencing for the diagnosis of. Utility of ces in consanguineous populations has not yet been determined on a large scale. Finding disease variants in mendelian disorders by using. Nextgeneration sequencing, whole exome sequencing, clinical applications, mendelian diseases introduction mendelian diseases, also known as monogenic diseases, are disorders caused by mutations in one gene and include diseases like thalassemia, cystic fibrosis, among others. Wholeexome sequencing reanalysis at 12 months boosts.