Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

Yong Hou; Kui Wu; Xulian Shi; Fuqiang Li; Luting Song; Hanjie Wu; Michael Dean; Guibo Li; Shirley Tsang; Runze Jiang; Xiaolong Zhang; Bo Li; Geng Liu; Niharika Bedekar; Na Lu; Guoyun Xie; Han Liang; Liao Chang; Ting Wang; Jianghao Chen; Yingrui Li; Xiuqing Zhang; Huanming Yang; Xun Xu; Ling Wang; Jun Wang

doi:10.1186/s13742-015-0068-3

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

Yong Hou, Kui Wu, Xulian Shi, Fuqiang Li, Luting Song, Hanjie Wu, Michael Dean, Guibo Li, Shirley Tsang, Runze Jiang, Xiaolong Zhang, Bo Li, Geng Liu, Niharika Bedekar, Na Lu, Guoyun Xie, Han Liang, Liao Chang, Ting Wang, Jianghao ChenYingrui Li, Xiuqing Zhang, Huanming Yang, Xun Xu, Ling Wang, Jun Wang

Genome Research and Molecular Bio Medicine

81 Citations (Scopus)

303 Downloads (Pure)

Abstract

BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed.

RESULTS: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2).

CONCLUSIONS: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.

Original language	English
Article number	37
Journal	GigaScience
Volume	4
Number of pages	16
ISSN	2047-217X
DOIs	https://doi.org/10.1186/s13742-015-0068-3
Publication status	Published - 2015

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Comparison of variations detection between whole-genome amplification methods used in single-cell resequencingFinal published version, 2.27 MBLicence: CC BY

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Hou, Y., Wu, K., Shi, X., Li, F., Song, L., Wu, H., Dean, M., Li, G., Tsang, S., Jiang, R., Zhang, X., Li, B., Liu, G., Bedekar, N., Lu, N., Xie, G., Liang, H., Chang, L., Wang, T., ... Wang, J. (2015). Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. GigaScience, 4, [37]. https://doi.org/10.1186/s13742-015-0068-3

Hou, Y, Wu, K, Shi, X, Li, F, Song, L, Wu, H, Dean, M, Li, G, Tsang, S, Jiang, R, Zhang, X, Li, B, Liu, G, Bedekar, N, Lu, N, Xie, G, Liang, H, Chang, L, Wang, T, Chen, J, Li, Y, Zhang, X, Yang, H, Xu, X, Wang, L & Wang, J 2015, 'Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing', GigaScience, vol. 4, 37. https://doi.org/10.1186/s13742-015-0068-3

@article{94d486eb30da43d7b3078696b3771d43,

title = "Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing",

abstract = "BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed.RESULTS: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2).CONCLUSIONS: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.",

author = "Yong Hou and Kui Wu and Xulian Shi and Fuqiang Li and Luting Song and Hanjie Wu and Michael Dean and Guibo Li and Shirley Tsang and Runze Jiang and Xiaolong Zhang and Bo Li and Geng Liu and Niharika Bedekar and Na Lu and Guoyun Xie and Han Liang and Liao Chang and Ting Wang and Jianghao Chen and Yingrui Li and Xiuqing Zhang and Huanming Yang and Xun Xu and Ling Wang and Jun Wang",

year = "2015",

doi = "10.1186/s13742-015-0068-3",

language = "English",

volume = "4",

journal = "GigaScience",

issn = "2047-217X",

publisher = "BioMed Central Ltd.",

}

TY - JOUR

T1 - Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

AU - Hou, Yong

AU - Wu, Kui

AU - Shi, Xulian

AU - Li, Fuqiang

AU - Song, Luting

AU - Wu, Hanjie

AU - Dean, Michael

AU - Li, Guibo

AU - Tsang, Shirley

AU - Jiang, Runze

AU - Zhang, Xiaolong

AU - Li, Bo

AU - Liu, Geng

AU - Bedekar, Niharika

AU - Lu, Na

AU - Xie, Guoyun

AU - Liang, Han

AU - Chang, Liao

AU - Wang, Ting

AU - Chen, Jianghao

AU - Li, Yingrui

AU - Zhang, Xiuqing

AU - Yang, Huanming

AU - Xu, Xun

AU - Wang, Ling

AU - Wang, Jun

PY - 2015

Y1 - 2015

N2 - BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed.RESULTS: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2).CONCLUSIONS: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.

AB - BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed.RESULTS: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2).CONCLUSIONS: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.

U2 - 10.1186/s13742-015-0068-3

DO - 10.1186/s13742-015-0068-3

M3 - Journal article

C2 - 26251698

SN - 2047-217X

VL - 4

JO - GigaScience

JF - GigaScience

M1 - 37

ER -

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

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