Performance of four modern whole genome amplification methods for copy number variant detection in single cells

Whole genome amplification (WGA) has become an invaluable tool to perform copy number variation (CNV) detection in single, or a limited number of cells. Unfortunately, current WGA methods introduce representation bias that limits the detection of small CNVs. New WGA methods have been introduced that might have the potential to reduce this bias. We compared the performance of PicoPLEX DNA-Seq (Picoseq), DOPlify, REPLI-g and Ampli-1 WGA for aneuploidy screening and copy number analysis using shallow whole genome massively parallel sequencing (MPS), starting from single or a limited number of cells. Although the four WGA methods perform differently, they are all suited for this application.

[1]  N. Tõnisson,et al.  Somatic mosaicism for copy-neutral loss of heterozygosity and DNA copy number variations in the human genome , 2015, BMC Genomics.

[2]  Aviv Regev,et al.  Whole exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer , 2014, Nature Biotechnology.

[3]  I. Macaulay,et al.  Single Cell Genomics: Advances and Future Perspectives , 2014, PLoS genetics.

[4]  B. Menten,et al.  Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing , 2016, Scientific Reports.

[5]  Tom Sante,et al.  ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation , 2014, PloS one.

[6]  Sijia Lu,et al.  Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. , 2015, Annual review of genomics and human genetics.

[7]  Susan Done,et al.  Whole-Genome Amplification by Degenerate Oligonucleotide Primed PCR (DOP-PCR). , 2008, CSH protocols.

[8]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[9]  D. Cram,et al.  The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities. , 2015, Journal of genetics and genomics = Yi chuan xue bao.

[10]  A. Skowron,et al.  Methodology and applications , 1998 .

[11]  Ira M. Hall,et al.  Mosaic Copy Number Variation in Human Neurons , 2013, Science.

[12]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[13]  R. H. Kent,et al.  The Mean Square Successive Difference , 1941 .

[14]  Jenny C. Taylor,et al.  Clinical utilisation of a rapid low-pass whole genome sequencing technique for the diagnosis of aneuploidy in human embryos prior to implantation , 2014, Journal of Medical Genetics.

[15]  S. Kingsmore,et al.  Comprehensive human genome amplification using multiple displacement amplification , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Nicolò Manaresi,et al.  Molecular profiling of single circulating tumor cells with diagnostic intention , 2014, EMBO molecular medicine.

[17]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[18]  Yulan Sun,et al.  Tumor heterogeneity and circulating tumor cells. , 2016, Cancer letters.

[19]  M. Prokocimer,et al.  Establishment of a human T-acute lymphoblastic leukemia cell line with a (16;20) chromosome translocation. , 1990, Cancer genetics and cytogenetics.

[20]  B. Menten,et al.  Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts. , 2015, Fertility and sterility.

[21]  Pieter Wesseling,et al.  DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly , 2014, Genome research.

[22]  Chad A. Shaw,et al.  Evidence for feasibility of fetal trophoblastic cell‐based noninvasive prenatal testing† , 2016, Prenatal diagnosis.

[23]  Ting Wang,et al.  Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing , 2015, GigaScience.

[24]  Charles Gawad,et al.  A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods , 2014, PloS one.

[25]  Mingming Jia,et al.  COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer , 2010, Nucleic Acids Res..

[26]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[27]  B. Menten,et al.  Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method , 2015, Scientific Reports.

[28]  F. Kokocinski,et al.  Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos. , 2014, Fertility and sterility.