Literature DB >> 29067733

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

Laia Bassaganyas1, George Freedman2, Dedeepya Vaka3, Eunice Wan3, Richard Lao3, Flavia Chen3, Mark Kvale3, Robert J Currier4, Jennifer M Puck2,3, Pui-Yan Kwok1,3,5.   

Abstract

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.
© 2017 Wiley Periodicals, Inc.

Entities:  

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

Mesh:

Year:  2017        PMID: 29067733      PMCID: PMC5738671          DOI: 10.1002/humu.23356

Source DB:  PubMed          Journal:  Hum Mutat        ISSN: 1059-7794            Impact factor:   4.878


  8 in total

1.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

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

Authors:  Mads Vilhelm Hollegaard; Jonas Grauholm; Ronni Nielsen; Jakob Grove; Susanne Mandrup; David Michael Hougaard
Journal:  Mol Genet Metab       Date:  2013-06-13       Impact factor: 4.797

3.  Newborn screening blood spot analysis in the UK: influence of spot size, punch location and haematocrit.

Authors:  A J Lawson; L Bernstone; S K Hall
Journal:  J Med Screen       Date:  2015-06-25       Impact factor: 2.136

4.  The Spectrum of CFTR Variants in Nonwhite Cystic Fibrosis Patients: Implications for Molecular Diagnostic Testing.

Authors:  Iris Schrijver; Lynn Pique; Steve Graham; Michelle Pearl; Athena Cherry; Martin Kharrazi
Journal:  J Mol Diagn       Date:  2016-01       Impact factor: 5.568

5.  Birth prevalence of disorders detectable through newborn screening by race/ethnicity.

Authors:  Lisa Feuchtbaum; Jennifer Carter; Sunaina Dowray; Robert J Currier; Fred Lorey
Journal:  Genet Med       Date:  2012-07-05       Impact factor: 8.822

6.  High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA.

Authors:  Jesper Buchhave Poulsen; Francesco Lescai; Jakob Grove; Marie Bækvad-Hansen; Michael Christiansen; Christian Munch Hagen; Julian Maller; Christine Stevens; Shenting Li; Qibin Li; Jihua Sun; Jun Wang; Merete Nordentoft; Thomas Mears Werge; Preben Bo Mortensen; Anders Dupont Børglum; Mark Daly; David Michael Hougaard; Jonas Bybjerg-Grauholm; Mads Vilhelm Hollegaard
Journal:  PLoS One       Date:  2016-04-18       Impact factor: 3.240

7.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937

8.  Influence of Hematocrit and Total-Spot Volume on Performance Characteristics of Dried Blood Spots for Newborn Screening.

Authors:  Elizabeth M Hall; Sharon R Flores; Víctor R De Jesús
Journal:  Int J Neonatal Screen       Date:  2015-08-21
  8 in total
  15 in total

Review 1.  Newborn screening for severe combined immunodeficiency and T-cell lymphopenia.

Authors:  Jennifer M Puck
Journal:  Immunol Rev       Date:  2019-01       Impact factor: 12.988

2.  Early diagnosis of Pearson syndrome in neonatal intensive care following rapid mitochondrial genome sequencing in tandem with exome sequencing.

Authors:  Lauren S Akesson; Stefanie Eggers; Clare J Love; Belinda Chong; Emma I Krzesinski; Natasha J Brown; Tiong Y Tan; Christopher M Richmond; David R Thorburn; John Christodoulou; Matthew F Hunter; Sebastian Lunke; Zornitza Stark
Journal:  Eur J Hum Genet       Date:  2019-07-29       Impact factor: 4.246

3.  Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project.

Authors:  Tamara S Roman; Stephanie B Crowley; Myra I Roche; Ann Katherine M Foreman; Julianne M O'Daniel; Bryce A Seifert; Kristy Lee; Alicia Brandt; Chelsea Gustafson; Daniela M DeCristo; Natasha T Strande; Lori Ramkissoon; Laura V Milko; Phillips Owen; Sayanty Roy; Mai Xiong; Ryan S Paquin; Rita M Butterfield; Megan A Lewis; Katherine J Souris; Donald B Bailey; Christine Rini; Jessica K Booker; Bradford C Powell; Karen E Weck; Cynthia M Powell; Jonathan S Berg
Journal:  Am J Hum Genet       Date:  2020-08-26       Impact factor: 11.025

Review 4.  The use of dried blood spots for characterizing children's exposure to organic environmental chemicals.

Authors:  Dana Boyd Barr; Kurunthachalam Kannan; Yuxia Cui; Lori Merrill; Lauren M Petrick; John D Meeker; Timothy R Fennell; Elaine M Faustman
Journal:  Environ Res       Date:  2021-01-25       Impact factor: 6.498

5.  Using dried blood spot samples from a trio for linked-read whole-exome sequencing.

Authors:  Ólavur Mortensen; Leivur Nattestad Lydersen; Katrin Didriksen Apol; Guðrið Andorsdóttir; Bjarni Á Steig; Noomi Oddmarsdóttir Gregersen
Journal:  Eur J Hum Genet       Date:  2019-02-14       Impact factor: 4.246

6.  The role of exome sequencing in newborn screening for inborn errors of metabolism.

Authors:  Jennifer M Puck; Steven E Brenner; Aashish N Adhikari; Renata C Gallagher; Yaqiong Wang; Robert J Currier; George Amatuni; Laia Bassaganyas; Flavia Chen; Kunal Kundu; Mark Kvale; Sean D Mooney; Robert L Nussbaum; Savanna S Randi; Jeremy Sanford; Joseph T Shieh; Rajgopal Srinivasan; Uma Sunderam; Hao Tang; Dedeepya Vaka; Yangyun Zou; Barbara A Koenig; Pui-Yan Kwok; Neil Risch
Journal:  Nat Med       Date:  2020-08-10       Impact factor: 53.440

7.  High Incidence of Severe Combined Immunodeficiency Disease in Saudi Arabia Detected Through Combined T Cell Receptor Excision Circle and Next Generation Sequencing of Newborn Dried Blood Spots.

Authors:  Hamoud Al-Mousa; Ghadah Al-Dakheel; Amal Jabr; Fahd Elbadaoui; Mohamed Abouelhoda; Mansoor Baig; Dorota Monies; Brian Meyer; Abbas Hawwari; Majed Dasouki
Journal:  Front Immunol       Date:  2018-04-16       Impact factor: 8.786

8.  Second-Tier Next Generation Sequencing Integrated in Nationwide Newborn Screening Provides Rapid Molecular Diagnostics of Severe Combined Immunodeficiency.

Authors:  Janne Strand; Kiran Aftab Gul; Hans Christian Erichsen; Emma Lundman; Mona C Berge; Anette K Trømborg; Linda K Sørgjerd; Mari Ytre-Arne; Silje Hogner; Ruth Halsne; Hege Junita Gaup; Liv T Osnes; Grete A B Kro; Hanne S Sorte; Lars Mørkrid; Alexander D Rowe; Trine Tangeraas; Jens V Jørgensen; Charlotte Alme; Trude E H Bjørndalen; Arild E Rønnestad; Astri M Lang; Terje Rootwelt; Jochen Buechner; Torstein Øverland; Tore G Abrahamsen; Rolf D Pettersen; Asbjørg Stray-Pedersen
Journal:  Front Immunol       Date:  2020-07-09       Impact factor: 7.561

9.  Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia.

Authors:  Gang Peng; Peidong Shen; Neeru Gandotra; Anthony Le; Eula Fung; Laura Jelliffe-Pawlowski; Ronald W Davis; Gregory M Enns; Hongyu Zhao; Tina M Cowan; Curt Scharfe
Journal:  Genet Med       Date:  2018-09-13       Impact factor: 8.822

10.  Postmortem whole-genome sequencing on a dried blood spot identifies a novel homozygous SUOX variant causing isolated sulfite oxidase deficiency.

Authors:  Mallory J Owen; Jerica Lenberg; Annette Feigenbaum; Jeffrey Gold; Kevin Chau; Zaira Bezares-Orin; Yan Ding; Shimul Chowdhury; Stephen F Kingsmore
Journal:  Cold Spring Harb Mol Case Stud       Date:  2021-06-11
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.