Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing

Lind, Curt; Ferriola, Deborah; Mackiewicz, Katarzyna; Heron, S.; Rogers, Marianne; Slavich, Larissa; Walker, Russell; Hsiao, Tom; McLaughlin, Laura; D’Arcy, Monica; Gai, Xiaowu; Goodridge, Damian; Sayer, D.; Monos, Dimitri

doi:10.1016/j.humimm.2010.06.016

Cited by 135 publications

(97 citation statements)

References 34 publications

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“…• Multi-gene diagnostic panels (Morgan et al 2010) • Achieving a molecular diagnosis for rare genetic diseases (Lupski et al 2010;Ng et al 2010a, b;Worthey et al 2011;Vissers et al 2010) • Tissue matching and HLA-typing (Bentley et al 2009;Gabriel et al 2009;Lind et al 2010) • Non-invasive prenatal diagnosis (Chiu et al 2008;Fan et al 2008;Lo et al 2010) • Quantifying the burden of disease from solid tumours (Leary et al 2010;McBride et al 2010) and • Cancer genome profiling leading to stratified treatment regimens Diamandis et al 2010;Stratton et al 2009) RNA sequencing (RNA-seq) and chromatin immunoprecipitation (ChIP) sequencing can also be used to study gene expression and for detection of somatic mutations, gene fusions, and other non-mutational events, an understanding of which can have an impact on management of diseases such as cancer (Cowin et al 2010;Robison 2010). However, numerous barriers to clinical translation still exist, including: validation of the technology; standardisation of the analysis pipeline; integration of information from the numerous databases of genomic variation; building a robust evidence base to allow clinical interpretation of novel variants; developing a service delivery infrastructure that can capitalise upon the high-throughput advantages of new sequencing technologies; providing an appropriately skilled health care workforce to deal with genomic medicine; and addressing the numerous ethical, legal and social implications of sequencing, storing and accessing whole genomes.…”

Section: Resultsmentioning

confidence: 99%

Review of massively parallel DNA sequencing technologies

Moorthie

Mattocks

Wright

2011

HUGO J

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Since the development of technologies that can determine the base-pair sequence of DNA, the ability to sequence genes has contributed much to science and medicine. However, it has remained a relatively costly and laborious process, hindering its use as a routine biomedical tool. Recent times are seeing rapid developments in this field, both in the availability of novel sequencing platforms, as well as supporting technologies involved in processes such as targeting and data analysis. This is leading to significant reductions in the cost of sequencing a human genome and the potential for its use as a routine biomedical tool. This review is a snapshot of this rapidly moving field examining the current state of the art, forthcoming developments and some of the issues still to be resolved prior to the use of new sequencing technologies in routine clinical diagnosis.

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Section: Resultsmentioning

confidence: 99%

Review of massively parallel DNA sequencing technologies

Moorthie

Mattocks

Wright

2011

HUGO J

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“…16 Epigenomic techniques include whole methylome-bisulfate sequencing (WM-Bseq), chromatin-immunoprecipitation sequencing (ChIP-seq), open chromatin sequencing (DNase-seq, Faire-Seq), long-range genome interaction mapping (3C, 5C, Hi-C, Chia-PET). 17 that non-HLA-A, B, C, DQB1 and DRB1 genetic differences may be important in allorecognition. For example, HLA-DP, which is poorly expressed on the surface of lymphocytes, was not historically considered in matching.…”

Section: Box 1 New Genomics Technology In Hctmentioning

confidence: 99%

“…SGS makes targeted sequencing of entire HLA genes feasible with minimal increase in cost. 17 In light of the recent findings that HLA-DP and other non-classical HLA mismatches also correlate with increased risk of TRM and GVHD, additional genetic information captured with SGS-based HLA typing may have clinical utility, particularly where multiple equivocally matched donors are identified based on classical HLA typing.…”

Section: Box 1 New Genomics Technology In Hctmentioning

confidence: 99%

Making the genomic leap in HCT: application of second-generation sequencing to clinical advances in hematopoietic cell transplantation

Levine

Hákonarson

et al. 2013

Eur J Hum Genet

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Recent developments in second-generation sequencing (SGS) technologies provide an avenue for achieving rapid and accurate high-throughput analysis of human and microbial genomic diversity. SGS technologies have the potential to transform existing medical management of complex and life-threatening medical conditions by enabling clinicians to develop disease-targeted clinical care plans for each patient. In this review, we outline how innovative SGS-based approaches can improve the care of recipients of allogeneic hematopoietic cell transplantation (HCT), a life-saving procedure that carries a 1-year mortality risk of over 30%. We specifically evaluate foreseeable applications of SGS-based technology in facilitating rapid, phase-sensitive human leukocyte antigen (HLA) typing, assessment of non-HLA genomic compatibility, identifying patients at high risk for adverse drug reactions, and post-HCT monitoring for engraftment, minimal residual disease and infection. We conclude that innovative SGS approaches have the capacity to revolutionize the HCT recipient risk assessment process, support non-invasive clinical monitoring and improve patient outcomes, thereby setting the stage for a new era of genomically informed patient-centered medicine.

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“…[22][23][24][25] Following amplification, all products are quantified and normalized to equimolar amounts, which is time-consuming when handling large numbers of samples. The goal of this study was to design an accurate, fast, and costefficient tool for molecular testing of all known LCA genes using MPS.…”

Section: Original Research Articlementioning

confidence: 99%

Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis

Coppieters

Wilde

Lefever

et al. 2012

Genetics in Medicine

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Purpose: Leber congenital amaurosis (LCA) is a rare congenital retinal dystrophy associated with 16 genes. Recent breakthroughs in LCA gene therapy offer the first prospect of treating inherited blindness, which requires an unequivocal and early molecular diagnosis. While present genetic tests do not address this due to a tremendous genetic heterogeneity, massively parallel sequencing (MPS) strategies might bring a solution. Here, we developed a comprehensive molecular test for LCA based on targeted MPS of all exons of 16 known LCA genes. methods:We designed a unique and flexible workflow for targeted resequencing of all 236 exons from 16 LCA genes based on quantitative PCR (qPCR) amplicon ligation, shearing, and parallel sequencing of multiple patients on a single lane of a short-read sequencer. Twenty-two prescreened LCA patients were included, five of whom had a known molecular cause.Results: Validation of 107 variations was performed as proof of concept. In addition, the causal genetic defect and a single heterozygous mutation were identified in 3 and 5, respectively, of 17 patients without previously identified mutations. conclusion:We propose a novel targeted MPS-based approach that is suitable for accurate, fast, and cost-effective early molecular testing in LCA, and easily applicable in other genetic disorders.Genet Med 2012:14(6):576-585

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Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing

Cited by 135 publications

References 34 publications

Review of massively parallel DNA sequencing technologies

Review of massively parallel DNA sequencing technologies

Making the genomic leap in HCT: application of second-generation sequencing to clinical advances in hematopoietic cell transplantation

Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis

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