Whole exome and whole genome sequencing with dried blood spot DNA without whole genome amplification

被引：30

作者：

Bassaganyas, Laia ^{[1
]}

Freedman, George ^{[2
]}

Vaka, Dedeepya ^{[3
]}

Wan, Eunice ^{[3
]}

Lao, Richard ^{[3
]}

Chen, Flavia ^{[3
]}

Kvale, Mark ^{[3
]}

Currier, Robert J. ^{[4
]}

Puck, Jennifer M. ^{[2
,3
]}

Kwok, Pui-Yan ^{[1
,3
,5
]}

机构：

[1] Univ Calif San Francisco, Cardiovasc Res Inst, San Francisco, CA 94143 USA

[2] Univ Calif San Francisco, Dept Pediat, San Francisco, CA USA

[3] Univ Calif San Francisco, Inst Human Genet, San Francisco, CA 94143 USA

[4] Calif Dept Publ Hlth, Genet Dis Screening Program, Richmond, CA USA

[5] Univ Calif San Francisco, Dept Dermatol, San Francisco, CA 94143 USA

来源：

HUMAN MUTATION | 2018年 / 39卷 / 01期

基金：

美国国家卫生研究院;

关键词：

dried blood spot DNA preparation; newborn screening; WES; whole exome sequencing; WGS; whole genome sequencing;

D O I：

10.1002/humu.23356

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Newborn screening (NBS) for rare conditions is performed in all 50 states in the USA. We have partnered with the California Department of Public Health Genetic Disease Laboratory to determine whether sufficient DNA can be extracted from archived dried blood spots (DBS) for next-generation sequencing in the hopes that next-generation sequencing can play a role in NBS. We optimized the DNA extraction and sequencing library preparation protocols for residual infant DBS archived over 20 years ago and successfully obtained acceptable whole exome and whole genome sequencing data. This sequencing study using DBS DNA without whole genome amplification prior to sequencing library preparation provides evidence that properly stored residual newborn DBS are a satisfactory source of DNA for genetic studies.

引用

页码：167 / 171

页数：5

共 8 条

[1] Birth prevalence of disorders detectable through newborn screening by race/ethnicity [J].

Feuchtbaum, Lisa ;

Carter, Jennifer ;

Dowray, Sunaina ;

Currier, Robert J. ;

Lorey, Fred .

GENETICS IN MEDICINE, 2012, 14 (11) :937-945

[2]

Hall EM, 2015, INT J NEONAT SCREEN, V1, P69, DOI 10.3390/ijns1020069

[3] Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing [J].

Hollegaard, Mads Vilhelm ;

Grauholm, Jonas ;

Nielsen, Ronni ;

Grove, Jakob ;

Mandrup, Susanne ;

Hougaard, David Michael .

MOLECULAR GENETICS AND METABOLISM, 2013, 110 (1-2) :65-72

[4] Newborn screening blood spot analysis in the UK: influence of spot size, punch location and haematocrit [J].

Lawson, A. J. ;

Bernstone, L. ;

Hall, S. K. .

JOURNAL OF MEDICAL SCREENING, 2016, 23 (01) :7-16

[5] Fast and accurate long-read alignment with Burrows-Wheeler transform [J].

Li, Heng ;

Durbin, Richard .

BIOINFORMATICS, 2010, 26 (05) :589-595

[6] The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data [J].

McKenna, Aaron ;

Hanna, Matthew ;

Banks, Eric ;

Sivachenko, Andrey ;

Cibulskis, Kristian ;

Kernytsky, Andrew ;

Garimella, Kiran ;

Altshuler, David ;

Gabriel, Stacey ;

Daly, Mark ;

DePristo, Mark A. .

GENOME RESEARCH, 2010, 20 (09) :1297-1303

[7] High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA [J].

Poulsen, Jesper Buchhave ;

Lescai, Francesco ;

Grove, Jakob ;

Baekvad-Hansen, Marie ;

Christiansen, Michael ;

Hagen, Christian Munch ;

Maller, Julian ;

Stevens, Christine ;

Li, Shenting ;

Li, Qibin ;

Sun, Jihua ;

Wang, Jun ;

Nordentoft, Merete ;

Werge, Thomas Mears ;

Mortensen, Preben Bo ;

Borglum, Anders Dupont ;

Daly, Mark ;

Hougaard, David Michael ;

Bybjerg-Grauholm, Jonas ;

Hollegaard, Mads Vilhelm .

PLOS ONE, 2016, 11 (04)

[8] The Spectrum of CFTR Variants in Nonwhite Cystic Fibrosis Patients Implications for Molecular Diagnostic Testing [J].

Schrijver, Iris ;

Pique, Lynn ;

Graham, Steve ;

Pearl, Michelle ;

Cherry, Athena ;

Kharrazi, Martin .

JOURNAL OF MOLECULAR DIAGNOSTICS, 2016, 18 (01) :39-50

← 1 →