SwePub
Sök i LIBRIS databas

  Extended search

onr:"swepub:oai:DiVA.org:uu-462226"
 

Search: onr:"swepub:oai:DiVA.org:uu-462226" > The SEQC2 epigenomi...

  • 1 of 1
  • Previous record
  • Next record
  •    To hitlist
  • Foox, JonathanWeill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA. (author)

The SEQC2 epigenomics quality control (EpiQC) study

  • Article/chapterEnglish2021

Publisher, publication year, extent ...

  • 2021-12-06
  • BioMed Central (BMC),2021
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:uu-462226
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-462226URI
  • https://doi.org/10.1186/s13059-021-02529-2DOI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • Correction in: Genome Biology, Volume 22, Issue 1, Article Number 350, DOI 10.1186/s13059-021-02573-y
  • BackgroundCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.ResultsEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.ConclusionsThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Nordlund, JessicaUppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands(Swepub:uu)jesno775 (author)
  • Lalancette, ClaudiaUniv Michigan Med, BRCF Epigen Core, Ann Arbor, MI 48109 USA. (author)
  • Gong, TingUniv Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA. (author)
  • Lacey, MichelleTulane Univ, New Orleans, LA 70118 USA. (author)
  • Lent, SamanthaAbbVie Genom Res Ctr, 1 N Waukegan Rd, N Chicago, IL 60036 USA. (author)
  • Langhorst, Bradley W.New England Biolabs Inc, Ipswich, MA 01938 USA. (author)
  • Ponnaluri, V. K. ChaithanyaNew England Biolabs Inc, Ipswich, MA 01938 USA. (author)
  • Williams, LouiseNew England Biolabs Inc, Ipswich, MA 01938 USA. (author)
  • Padmanabhan, Karthik RamaswamyUniv Michigan Med, BRCF Epigen Core, Ann Arbor, MI 48109 USA. (author)
  • Cavalcante, RaymondUniv Michigan Med, BRCF Epigen Core, Ann Arbor, MI 48109 USA. (author)
  • Lundmark, AndersUppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands(Swepub:uu)andlu294 (author)
  • Butler, DanielWeill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA. (author)
  • Mozsary, ChristopherWeill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA. (author)
  • Gurvitch, JustinWeill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA. (author)
  • Greally, John M.Albert Einstein Coll Med, Bronx, NY 10461 USA. (author)
  • Suzuki, MasakoAlbert Einstein Coll Med, Bronx, NY 10461 USA. (author)
  • Menor, MarkUniv Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA. (author)
  • Nasu, MasakiUniv Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA. (author)
  • Alonso, AliciaWeill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA. (author)
  • Sheridan, CarolineWeill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.;Weill Cornell Med, Div Hematol Oncol, Dept Med, Epigen Core Facil, New York, NY USA. (author)
  • Scherer, AndreasEATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;Univ Helsinki, Inst Mol Med Finland FIMM, Helsinki, Finland. (author)
  • Bruinsma, StephenIllumina Inc, Madison, WI 53705 USA. (author)
  • Golda, GosiaJagiellonian Univ, Fac Biochem Biophys & Biotechnol, Krakow, Poland. (author)
  • Muszynska, AgataJagiellonian Univ, Malopolska Ctr Biotechnol, Krakow, Poland. (author)
  • Labaj, Pawel P.Jagiellonian Univ, Malopolska Ctr Biotechnol, Krakow, Poland. (author)
  • Campbell, Matthew A.New England Biolabs Inc, Ipswich, MA 01938 USA. (author)
  • Wos, FrankNew York Genome Ctr, New York, NY 10013 USA. (author)
  • Raine, AmandaUppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinska vetenskaper,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands(Swepub:uu)amrai226 (author)
  • Liljedahl, UlrikaUppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands(Swepub:uu)ullil257 (author)
  • Axelsson, TomasUppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands(Swepub:uu)toaxe957 (author)
  • Wang, CharlesLoma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA. (author)
  • Chen, ZhongLoma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA. (author)
  • Yang, ZhaoweiLoma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA.;Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Dept Allergy & Clin Immunol, State Key Lab Resp Dis,Affiliated Hosp 1, Guangzhou, Peoples R China. (author)
  • Li, JingLoma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA.;Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Dept Allergy & Clin Immunol, State Key Lab Resp Dis,Affiliated Hosp 1, Guangzhou, Peoples R China. (author)
  • Yang, XiaopengZhengzhou Univ, Dept Neurol, Affiliated Hosp 2, Zhengzhou 450014, Peoples R China. (author)
  • Wang, HongweiUniv Chicago, Dev Med, Chicago, IL 60637 USA. (author)
  • Melnick, AriWeill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA. (author)
  • Guo, ShangZhengzhou Univ, Affiliated Hosp 2, Shanghai 200233, Peoples R China. (author)
  • Blume, AlexanderMax Delbrueck Ctr Mol Med, Berlin Inst Med Syst Biol, Bioinformat & Omics Data Sci Platform, Berlin, Germany. (author)
  • Franke, VedranMax Delbrueck Ctr Mol Med, Berlin Inst Med Syst Biol, Bioinformat & Omics Data Sci Platform, Berlin, Germany. (author)
  • Ibanez de Caceres, InmaculadaEATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;IdiPAZ, Canc Epigenet Lab, INGEMM, Madrid, Spain. (author)
  • Rodriguez-Antolin, CarlosEATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;IdiPAZ, Canc Epigenet Lab, INGEMM, Madrid, Spain. (author)
  • Rosas, RocioEATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;IdiPAZ, Canc Epigenet Lab, INGEMM, Madrid, Spain. (author)
  • Davis, Justin WadeAbbVie Genom Res Ctr, 1 N Waukegan Rd, N Chicago, IL 60036 USA. (author)
  • Ishii, JenniferNew York Genome Ctr, New York, NY 10013 USA. (author)
  • Megherbi, Dalila B.Univ Massachusetts Lowell, Francis Coll Engn, CMINDS Res Ctr, Lowell, MA 01854 USA. (author)
  • Xiao, WenmingUS FDA, Ctr Devices & Radiol Hlth, 10903 New Hampshire Ave, Silver Spring, MD 20993 USA. (author)
  • Liao, WillNew York Genome Ctr, New York, NY 10013 USA. (author)
  • Xu, JoshuaUS FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA. (author)
  • Hong, HuixiaoUS FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA. (author)
  • Ning, BaitangUS FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA. (author)
  • Tong, WeidaUS FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA. (author)
  • Akalin, AltunaMax Delbrueck Ctr Mol Med, Berlin Inst Med Syst Biol, Bioinformat & Omics Data Sci Platform, Berlin, Germany. (author)
  • Wang, YunliangZhengzhou Univ, Affiliated Hosp 2, Shanghai 200233, Peoples R China. (author)
  • Deng, YoupingUniv Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA. (author)
  • Mason, Christopher E.Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA.;Feil Family Brain & Mind Res Inst, New York, NY 10065 USA.;Weill Cornell Med, WorldQuant Initiat Quantitat Predict, New York, NY 10021 USA. (author)
  • Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA.Molekylär medicin (creator_code:org_t)

Related titles

  • In:Genome Biology: BioMed Central (BMC)22:11465-69061474-760X

Internet link

Find in a library

To the university's database

  • 1 of 1
  • Previous record
  • Next record
  •    To hitlist

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Close

Copy and save the link in order to return to this view