Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis.
Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis.
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DOI：
10.1186/s13073-017-0479-0
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发表时间：
2017-10-25
期刊：
影响因子：
12.3
通讯作者：
Vilain E
中科院分区：
文献类型：
--
作者：
Barseghyan H;Tang W;Wang RT;Almalvez M;Segura E;Bramble MS;Lipson A;Douine ED;Lee H;Délot EC;Nelson SF;Vilain E
大规模并行 DNA 测序（例如外显子组测序）已成为识别导致患者表型的致病变异的常规临床程序。外显子组测序能够可靠地识别遗传和从头单核苷酸变异、小插入和缺失。然而，由于使用 100-300 bp 片段读取，该平台不能很好地灵敏地识别中到大的结构变异 (SV)，例如插入、删除、倒位和易位。为了克服这些限制，我们使用下一代作图 (NGM) 对纳米通道阵列中带有荧光标签的高分子量双链 DNA 分子（兆碱基大小）进行成像，以进行从头基因组组装。我们研究了该 NGM 平台在一系列诊断为杜氏肌营养不良症 (DMD) 的患者中识别致病性 SV 的能力，这些患者由于涉及 DMD 基因的大量缺失、插入和倒位而导致。我们确定了 DMD 中的删除、重复和反转断点。缺失的大小在 45-250 Kbp 范围内，而识别出的插入大小约为 13 Kbp。与当前基于聚合酶链式反应 (PCR) 的临床技术相比，该方法改进了缺失病例内含子内断裂点的位置。在 DMD 患者的已知携带者母亲中检测到杂合 SV，证明该方法能够确定大 SV 携带者状态。该方法还能够识别涉及 DMD 基因的 5.1-Mbp 倒位，先前通过 RNA 测序识别出该倒位。我们展示了 NGM 技术检测致病性结构变异的能力，否则基于 PCR 的技术或染色体微阵列会漏掉这些变异。 NGM 由于能够灵敏地识别大的基因组变异，有望成为临床遗传诊断策略和研究的新工具。本文的在线版本 (doi:10.1186/s13073-017-0479-0) 包含补充材料，可供授权用户使用。
Massively parallel DNA sequencing, such as exome sequencing, has become a routine clinical procedure to identify pathogenic variants responsible for a patient’s phenotype. Exome sequencing has the capability of reliably identifying inherited and de novo single-nucleotide variants, small insertions, and deletions. However, due to the use of 100–300-bp fragment reads, this platform is not well powered to sensitively identify moderate to large structural variants (SV), such as insertions, deletions, inversions, and translocations. To overcome these limitations, we used next-generation mapping (NGM) to image high molecular weight double-stranded DNA molecules (megabase size) with fluorescent tags in nanochannel arrays for de novo genome assembly. We investigated the capacity of this NGM platform to identify pathogenic SV in a series of patients diagnosed with Duchenne muscular dystrophy (DMD), due to large deletions, insertion, and inversion involving the DMD gene. We identified deletion, duplication, and inversion breakpoints within DMD. The sizes of deletions were in the range of 45–250 Kbp, whereas the one identified insertion was approximately 13 Kbp in size. This method refined the location of the break points within introns for cases with deletions compared to current polymerase chain reaction (PCR)-based clinical techniques. Heterozygous SV were detected in the known carrier mothers of the DMD patients, demonstrating the ability of the method to ascertain carrier status for large SV. The method was also able to identify a 5.1-Mbp inversion involving the DMD gene, previously identified by RNA sequencing. We showed the ability of NGM technology to detect pathogenic structural variants otherwise missed by PCR-based techniques or chromosomal microarrays. NGM is poised to become a new tool in the clinical genetic diagnostic strategy and research due to its ability to sensitively identify large genomic variations. The online version of this article (doi:10.1186/s13073-017-0479-0) contains supplementary material, which is available to authorized users.
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影响因子：
46.9
作者：
通讯作者：
--
影响因子：
23.9
作者：
Young CS;Hicks MR;Ermolova NV;Nakano H;Jan M;Younesi S;Karumbayaram S;Kumagai-Cresse C;Wang D;Zack JA;Kohn DB;Nakano A;Nelson SF;Miceli MC;Spencer MJ;Pyle AD
通讯作者：
Pyle AD
通过种群规模的基因组测序来映射拷贝数变化。
影响因子：
64.8
作者：
Mills, Ryan E.;Walter, Klaudia;Stewart, Chip;Handsaker, Robert E.;Chen, Ken;Alkan, Can;Abyzov, Alexej;Yoon, Seungtai Chris;Ye, Kai;Cheetham, R. Keira;Chinwalla, Asif;Conrad, Donald F.;Fu, Yutao;Grubert, Fabian;Hajirasouliha, Iman;Hormozdiari, Fereydoun;Iakoucheva, Lilia M.;Iqbal, Zamin;Kang, Shuli;Kidd, Jeffrey M.;Konkel, Miriam K.;Korn, Joshua;Khurana, Ekta;Kural, Deniz;Lam, Hugo Y. K.;Leng, Jing;Li, Ruiqiang;Li, Yingrui;Lin, Chang-Yun;Luo, Ruibang;Mu, Xinmeng Jasmine;Nemesh, James;Peckham, Heather E.;Rausch, Tobias;Scally, Aylwyn;Shi, Xinghua;Stromberg, Michael P.;Stuetz, Adrian M.;Urban, Alexander Eckehart;Walker, Jerilyn A.;Wu, Jiantao;Zhang, Yujun;Zhang, Zhengdong D.;Batzer, Mark A.;Ding, Li;Marth, Gabor T.;McVean, Gil;Sebat, Jonathan;Snyder, Michael;Wang, Jun;Ye, Kenny;Eichler, Evan E.;Gerstein, Mark B.;Hurles, Matthew E.;Lee, Charles;McCarroll, Steven A.;Korbel, Jan O.
通讯作者：
Korbel, Jan O.
TREAT-NMD DMD 全球数据库：分析 7,000 多个杜氏肌营养不良症突变。
影响因子：
3.9
作者：
Bladen, Catherine L.;Salgado, David;Monges, Soledad;Foncuberta, Maria E.;Kekou, Kyriaki;Kosma, Konstantina;Dawkins, Hugh;Lamont, Leanne;Roy, Anna J.;Chamova, Teodora;Guergueltcheva, Velina;Chan, Sophelia;Korngut, Lawrence;Campbell, Craig;Dai, Yi;Wang, Jen;Barisic, Nina;Brabec, Petr;Lahdetie, Jaana;Walter, Maggie C.;Schreiber-Katz, Olivia;Karcagi, Veronika;Garami, Marta;Viswanathan, Venkatarman;Bayat, Farhad;Buccella, Filippo;Kimura, En;Koeks, Zaida;van den Bergen, Janneke C.;Rodrigues, Miriam;Roxburgh, Richard;Lusakowska, Anna;Kostera-Pruszczyk, Anna;Zimowski, Janusz;Santos, Rosario;Neagu, Elena;Artemieva, Svetlana;Rasic, Vedrana Milic;Vojinovic, Dina;Posada, Manuel;Bloetzer, Clemens;Jeannet, Pierre-Yves;Joncourt, Franziska;Diaz-Manera, Jordi;Gallardo, Eduard;Karaduman, A. Ayse;Topaloglu, Haluk;El Sherif, Rasha;Stringer, Angela;Shatillo, Andriy V.;Martin, Ann S.;Peay, Holly L.;Bellgard, Matthew I.;Kirschner, Jan;Flanigan, Kevin M.;Straub, Volker;Bushby, Kate;Verschuuren, Jan;Aartsma-Rus, Annemieke;Beroud, Christophe;Lochmueller, Hanns
通讯作者：
Lochmueller, Hanns
DOI：
10.1056/nejmoa1306555
发表时间：
2013-10-17
期刊：
The New England journal of medicine
影响因子：
--
作者：
Yang Y;Muzny DM;Reid JG;Bainbridge MN;Willis A;Ward PA;Braxton A;Beuten J;Xia F;Niu Z;Hardison M;Person R;Bekheirnia MR;Leduc MS;Kirby A;Pham P;Scull J;Wang M;Ding Y;Plon SE;Lupski JR;Beaudet AL;Gibbs RA;Eng CM
通讯作者：
Eng CM