kth.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Comparison of whole genome amplification techniques for human single cell exome sequencing
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Show others and affiliations
2017 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 12, no 2, article id e0171566Article in journal (Refereed) Published
Abstract [en]

Background Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. Results The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. Discussion In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE , 2017. Vol. 12, no 2, article id e0171566
National Category
Basic Medicine
Identifiers
URN: urn:nbn:se:kth:diva-204082DOI: 10.1371/journal.pone.0171566ISI: 000394424500038PubMedID: 28207771Scopus ID: 2-s2.0-85013058522OAI: oai:DiVA.org:kth-204082DiVA, id: diva2:1085458
Note

QC 20170329

Available from: 2017-03-29 Created: 2017-03-29 Last updated: 2024-03-18Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMedScopus

Authority records

Borgström, ErikLundeberg, Joakim

Search in DiVA

By author/editor
Borgström, ErikLundeberg, Joakim
By organisation
Gene TechnologyScience for Life Laboratory, SciLifeLab
In the same journal
PLOS ONE
Basic Medicine

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 111 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf