Inspecting Targeted Deep Sequencing of Whole Genome Amplified DNA Versus Fresh DNA for Somatic Mutation Detection: A Genetic Study in Myelodysplastic Syndrome Patients

被引:0
作者
Palomo, Laura [1 ]
Fuster-Tormo, Francisco [1 ]
Alvira, Daniel [1 ]
Adema, Vera [1 ,2 ]
Pilar Armengol, Maria [3 ]
Gomez-Marzo, Paula [1 ]
de Haro, Nuri [1 ]
Mallo, Mar [1 ]
Xicoy, Blanca [4 ]
Zamora, Lurdes [4 ]
Sole, Francesc [1 ]
机构
[1] Univ Autonoma Barcelona, ICO Hosp Germans Trias & Pujol, Josep Carreras Leukaemia Res Inst IJC, MDS Grp, Badalona, Barcelona, Spain
[2] Cleveland Clin, Taussig Canc Inst, Dept Translat Hematol & Oncol Res, Cleveland, OH 44106 USA
[3] Inst Invest Ciencies Salut Germans Trias & Pujol, Genom & Microscopy Facil, Badalona, Barcelona, Spain
[4] Univ Autonoma Barcelona, Josep Carreras Leukaemia Res Inst IJC, ICO Hosp Germans Trias & Pujol, Hematol Serv, Badalona, Barcelona, Spain
关键词
DNA banking; whole genome amplification; next-generation sequencing; targeted deep sequencing; myelodysplastic syndromes; SAMPLES;
D O I
10.1089/bio.2016.0094
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
Whole genome amplification (WGA) has become an invaluable method for preserving limited samples of precious stock material and has been used during the past years as an alternative tool to increase the amount of DNA before library preparation for next-generation sequencing. Myelodysplastic syndromes (MDS) are a group of clonal hematopoietic stem cell disorders characterized by presenting somatic mutations in several myeloid-related genes. In this work, targeted deep sequencing has been performed on four paired fresh DNA and WGA DNA samples from bone marrow of MDS patients, to assess the feasibility of using WGA DNA for detecting somatic mutations. The results of this study highlighted that, in general, the sequencing and alignment statistics of fresh DNA and WGA DNA samples were similar. However, after variant calling and when considering variants detected at all frequencies, there was a high level of discordance between fresh DNA and WGA DNA (overall, a higher number of variants was detected in WGA DNA). After proper filtering, a total of three somatic mutations were detected in the cohort. All somatic mutations detected in fresh DNA were also identified in WGA DNA and validated by whole exome sequencing.
引用
收藏
页码:360 / 365
页数:6
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