Advancing genetic testing for deafness with genomic technology.
Advancing genetic testing for deafness with genomic technology.
复制标题
DOI：
10.1136/jmedgenet-2013-101749
复制
发表时间：
2013-09
影响因子：
4
通讯作者：
Smith RJ
中科院分区：
文献类型：
--
作者：
Shearer AE;Black-Ziegelbein EA;Hildebrand MS;Eppsteiner RW;Ravi H;Joshi S;Guiffre AC;Sloan CM;Happe S;Howard SD;Novak B;Deluca AP;Taylor KR;Scheetz TE;Braun TA;Casavant TL;Kimberling WJ;Leproust EM;Smith RJ
非综合征性听力损失（NSHL）是人类最常见的感觉障碍。直到最近，其极端的遗传异质性还无法进行全面的基因检测。使用一个平台，耦合靶向基因组富集（TGE）和大规模平行测序（MPS），以测序所有基因的所有外显子涉及NSHL，我们测试了100人与假定的遗传NSHL，并在这样做建立测序要求的最大灵敏度和定义MPS质量评分指标，验证桑格验证的变体。我们检查了100个连续收集的先证者的DNA，这些先证者具有假定的遗传性NSHL，没有由于遗传、先前的基因检测或听力损失类型而被排除。我们使用可变池大小的捕获后多路复用进行TGE，然后进行Illumina测序。我们在一个高性能计算集群上开发了一个本地Galaxy安装，用于生物信息学分析。为了使用该平台获得最大的变体灵敏度，每个样品需要320 - 630万个总映射测序读数。质量评分分析表明，桑格验证是不需要的95%的变异。我们的总体诊断率为42%，但因临床特征而异，从不对称性听力损失患者的0%到双侧常染色体隐性NSHL患者的56%。这些发现将指导TGE和MPS策略在NSHL基因诊断中的应用。我们的诊断率强调了需要进一步研究遗传性耳聋，重点是新基因的识别和非外显子突变的作用，提高认识。我们确定的未解决的家庭为解决这些问题提供了宝贵的资源。
Non-syndromic hearing loss (NSHL) is the most common sensory impairment in humans. Until recently its extreme genetic heterogeneity precluded comprehensive genetic testing. Using a platform that couples targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) to sequence all exons of all genes implicated in NSHL, we test 100 persons with presumed genetic NSHL and in so doing establish sequencing requirements for maximum sensitivity and define MPS quality score metrics that obviate Sanger validation of variants. We examined DNA from 100 sequentially collected probands with presumed genetic NSHL without exclusions due to inheritance, previous genetic testing, or type of hearing loss. We performed TGE using post-capture multiplexing in variable pool sizes followed by Illumina sequencing. We developed a local Galaxy installation on a high performance-computing cluster for bioinformatics analysis. To obtain maximum variant sensitivity with this platform 3.2–6.3 million total mapped sequencing reads per sample are required. Quality score analysis showed that Sanger validation is not required for 95% of variants. Our overall diagnostic rate was 42% but varied by clinical features from 0% for persons with asymmetric hearing loss to 56% for persons with bilateral autosomal recessive NSHL. These findings will direct the use of TGE and MPS strategies for genetic diagnosis for NSHL. Our diagnostic rate highlights the need for further research on genetic deafness focused on novel gene identification and an improved understanding of the role of non-exonic mutations. The unsolved families we have identified provide a valuable resource to address these areas.
登录
查看更多内容
全基因组SNP基因分型鉴定立体纤维蛋白（Strc）基因是小儿双边感觉神经性听力障碍的主要因素。
影响因子：
2
作者：
Francey, Lauren J.;Conlin, Laura K.;Kadesch, Hanna E.;Clark, Dinah;Berrodin, Donna;Sun, Yi;Glessner, Joe;Hakonarson, Hakon;Jalas, Chaim;Landau, Chaim;Spinner, Nancy B.;Kenna, Margaret;Sagi, Michal;Rehm, Heidi L.;Krantz, Ian D.
通讯作者：
Krantz, Ian D.
DOI：
10.1126/science.1219240
发表时间：
2012-07-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Tennessen JA;Bigham AW;O'Connor TD;Fu W;Kenny EE;Gravel S;McGee S;Do R;Liu X;Jun G;Kang HM;Jordan D;Leal SM;Gabriel S;Rieder MJ;Abecasis G;Altshuler D;Nickerson DA;Boerwinkle E;Sunyaev S;Bustamante CD;Bamshad MJ;Akey JM;Broad GO;Seattle GO;NHLBI Exome Sequencing Project
通讯作者：
NHLBI Exome Sequencing Project
影响因子：
4.4
作者：
Nord AS;Lee M;King MC;Walsh T
通讯作者：
Walsh T
DOI：
10.1038/gim.2011.68
发表时间：
2012-04
期刊：
Genetics in medicine : official journal of the American College of Medical Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
4
作者：
Knijnenburg, J.;Oberstein, S. A. J. Lesnik;Szuhai, K.
通讯作者：
Szuhai, K.