Generating exome enriched sequencing libraries from formalin-fixed, paraffin-embedded tissue DNA for next-generation sequencing

Beth A. Marosy; Brian D. Craig; Kurt N. Hetrick; P. Dane Witmer; Hua Ling; Sean M. Griffith; Benjamin Myers; Elaine A. Ostrander; Janet L. Stanford; Lawrence C. Brody; Kimberly F. Doheny

doi:10.1002/cphg.27

Generating exome enriched sequencing libraries from formalin-fixed, paraffin-embedded tissue DNA for next-generation sequencing

Beth A. Marosy, Brian D. Craig, Kurt N. Hetrick, P. Dane Witmer, Hua Ling, Sean M. Griffith, Benjamin Myers, Elaine A. Ostrander, Janet L. Stanford, Lawrence C. Brody, Kimberly F. Doheny

School of Medicine

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

1 Scopus citations

Abstract

This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform.

Original language	English (US)
Pages (from-to)	18.10.1-18.10.25
Journal	Current protocols in human genetics
Volume	2017
DOIs	https://doi.org/10.1002/cphg.27
State	Published - Jan 1 2017

Keywords

DNA library preparation
DNA repair
FFPE
Next-generation sequencing
Whole exome sequencing

ASJC Scopus subject areas

Genetics
Genetics(clinical)

Access to Document

10.1002/cphg.27

Cite this

Marosy, B. A., Craig, B. D., Hetrick, K. N., Witmer, P. D., Ling, H., Griffith, S. M., Myers, B., Ostrander, E. A., Stanford, J. L., Brody, L. C., & Doheny, K. F. (2017). Generating exome enriched sequencing libraries from formalin-fixed, paraffin-embedded tissue DNA for next-generation sequencing. Current protocols in human genetics, 2017, 18.10.1-18.10.25. https://doi.org/10.1002/cphg.27

Marosy, BA, Craig, BD, Hetrick, KN, Witmer, PD, Ling, H, Griffith, SM, Myers, B, Ostrander, EA, Stanford, JL, Brody, LC & Doheny, KF 2017, 'Generating exome enriched sequencing libraries from formalin-fixed, paraffin-embedded tissue DNA for next-generation sequencing', Current protocols in human genetics, vol. 2017, pp. 18.10.1-18.10.25. https://doi.org/10.1002/cphg.27

@article{45ba697bf9f14994af19492b8fa3956b,

title = "Generating exome enriched sequencing libraries from formalin-fixed, paraffin-embedded tissue DNA for next-generation sequencing",

abstract = "This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform.",

keywords = "DNA library preparation, DNA repair, FFPE, Next-generation sequencing, Whole exome sequencing",

author = "Marosy, {Beth A.} and Craig, {Brian D.} and Hetrick, {Kurt N.} and Witmer, {P. Dane} and Hua Ling and Griffith, {Sean M.} and Benjamin Myers and Ostrander, {Elaine A.} and Stanford, {Janet L.} and Brody, {Lawrence C.} and Doheny, {Kimberly F.}",

note = "Publisher Copyright: {\textcopyright} 2017 by John Wiley & Sons, Inc.",

year = "2017",

month = jan,

day = "1",

doi = "10.1002/cphg.27",

language = "English (US)",

volume = "2017",

pages = "18.10.1--18.10.25",

journal = "Current protocols in human genetics",

issn = "1934-8266",

publisher = "John Wiley and Sons Inc.",

}

TY - JOUR

T1 - Generating exome enriched sequencing libraries from formalin-fixed, paraffin-embedded tissue DNA for next-generation sequencing

AU - Marosy, Beth A.

AU - Craig, Brian D.

AU - Hetrick, Kurt N.

AU - Witmer, P. Dane

AU - Ling, Hua

AU - Griffith, Sean M.

AU - Myers, Benjamin

AU - Ostrander, Elaine A.

AU - Stanford, Janet L.

AU - Brody, Lawrence C.

AU - Doheny, Kimberly F.

PY - 2017/1/1

Y1 - 2017/1/1

N2 - This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform.

AB - This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform.

KW - DNA library preparation

KW - DNA repair

KW - FFPE

KW - Next-generation sequencing

KW - Whole exome sequencing

UR - http://www.scopus.com/inward/record.url?scp=85029415152&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85029415152&partnerID=8YFLogxK

U2 - 10.1002/cphg.27

DO - 10.1002/cphg.27

M3 - Article

C2 - 28075488

AN - SCOPUS:85029415152

SN - 1934-8266

VL - 2017

SP - 18.10.1-18.10.25

JO - Current protocols in human genetics

JF - Current protocols in human genetics

ER -

Generating exome enriched sequencing libraries from formalin-fixed, paraffin-embedded tissue DNA for next-generation sequencing

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this