Systematic biases in DNA copy number originate from isolation procedures

Sebastiaan van Heesch; Michal Mokry; Veronika Boskova; Wade Junker; Rajdeep Mehon; Pim Toonen; Ewart de Bruijn; James D Shull; Timothy J Aitman; Edwin Cuppen; Victor Guryev

doi:10.1186/gb-2013-14-4-r33

Systematic biases in DNA copy number originate from isolation procedures

Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev

Research output: Contribution to journal › Article › peer-review

34 Citations (Scopus)

Abstract

BACKGROUND: The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.

RESULTS: While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.

CONCLUSION: These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.

Original language	English
Article number	R33
Pages (from-to)	R33
Journal	Genome biology
Volume	14
Issue number	4
DOIs	https://doi.org/10.1186/gb-2013-14-4-r33
Publication status	Published - 24 Apr 2013
Externally published	Yes

Keywords

Animals
Artifacts
Chemical Fractionation
DNA/genetics
DNA Copy Number Variations
Rats
Sensitivity and Specificity
Sequence Analysis, DNA/methods

Access to Document

10.1186/gb-2013-14-4-r33

Cite this

@article{5819ee1456c34981bd004dbaf1dbd960,

title = "Systematic biases in DNA copy number originate from isolation procedures",

abstract = "BACKGROUND: The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.RESULTS: While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.CONCLUSION: These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.",

keywords = "Animals, Artifacts, Chemical Fractionation, DNA/genetics, DNA Copy Number Variations, Rats, Sensitivity and Specificity, Sequence Analysis, DNA/methods",

author = "{van Heesch}, Sebastiaan and Michal Mokry and Veronika Boskova and Wade Junker and Rajdeep Mehon and Pim Toonen and {de Bruijn}, Ewart and Shull, {James D} and Aitman, {Timothy J} and Edwin Cuppen and Victor Guryev",

note = "Publisher Copyright: {\textcopyright} 2013 van Heesch et al.",

year = "2013",

month = apr,

day = "24",

doi = "10.1186/gb-2013-14-4-r33",

language = "English",

volume = "14",

pages = "R33",

journal = "Genome biology",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

number = "4",

}

TY - JOUR

T1 - Systematic biases in DNA copy number originate from isolation procedures

AU - van Heesch, Sebastiaan

AU - Mokry, Michal

AU - Boskova, Veronika

AU - Junker, Wade

AU - Mehon, Rajdeep

AU - Toonen, Pim

AU - de Bruijn, Ewart

AU - Shull, James D

AU - Aitman, Timothy J

AU - Cuppen, Edwin

AU - Guryev, Victor

PY - 2013/4/24

Y1 - 2013/4/24

N2 - BACKGROUND: The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.RESULTS: While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.CONCLUSION: These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.

AB - BACKGROUND: The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.RESULTS: While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.CONCLUSION: These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.

KW - Animals

KW - Artifacts

KW - Chemical Fractionation

KW - DNA/genetics

KW - DNA Copy Number Variations

KW - Rats

KW - Sensitivity and Specificity

KW - Sequence Analysis, DNA/methods

UR - http://www.scopus.com/inward/record.url?scp=84876670514&partnerID=8YFLogxK

U2 - 10.1186/gb-2013-14-4-r33

DO - 10.1186/gb-2013-14-4-r33

M3 - Article

C2 - 23618369

SN - 1474-7596

VL - 14

SP - R33

JO - Genome biology

JF - Genome biology

IS - 4

M1 - R33

ER -

Systematic biases in DNA copy number originate from isolation procedures

Abstract

Keywords

Access to Document

Fingerprint

Cite this