Search: WFRF:(Lack D.) >
Establishing commun...
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
-
- Fang, Li Tai (author)
- Roche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA.
-
- Zhu, Bin (author)
- NCI, Div Canc Epidemiol & Genet, NIH, Bethesda, MD 20892 USA.
-
- Zhao, Yongmei (author)
- Frederick Natl Lab Canc Res, Adv Biomed & Computat Sci, Biomed Informat & Data Sci Directorate, Frederick, MD USA.
-
show more...
-
- Chen, Wanqiu (author)
- Loma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA.
-
- Yang, Zhaowei (author)
- Loma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA.;Guangzhou Med Univ, Affiliated Hosp 1, Guangzhou Inst Resp Hlth,Dept Allergy & Clin Immu, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou, Peoples R China.
-
- Kerrigan, Liz (author)
- ATCC Amer Type Culture Collect, Manassas, VA USA.
-
- Langenbach, Kurt (author)
- ATCC Amer Type Culture Collect, Manassas, VA USA.
-
- de Mars, Maryellen (author)
- ATCC Amer Type Culture Collect, Manassas, VA USA.
-
- Lu, Charles (author)
- AbbVie, Genom Res Ctr GRC, Computat Genom, N Chicago, IL 60064 USA.
-
- Idler, Kenneth (author)
- AbbVie, Genom Res Ctr GRC, Computat Genom, N Chicago, IL 60064 USA.
-
- Jacob, Howard (author)
- AbbVie, Genom Res Ctr GRC, Computat Genom, N Chicago, IL 60064 USA.
-
- Zheng, Yuanting (author)
- Fudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China.
-
- Ren, Luyao (author)
- Fudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China.
-
- Yu, Ying (author)
- Fudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China.
-
- Jaeger, Erich (author)
- Illumina Inc, Foster City, CA USA.
-
- Schroth, Gary P. (author)
- Illumina Inc, Foster City, CA USA.
-
- Abaan, Ogan D. (author)
- Illumina Inc, Foster City, CA USA.
-
- Talsania, Keyur (author)
- Frederick Natl Lab Canc Res, Adv Biomed & Computat Sci, Biomed Informat & Data Sci Directorate, Frederick, MD USA.
-
- Lack, Justin (author)
- Frederick Natl Lab Canc Res, Adv Biomed & Computat Sci, Biomed Informat & Data Sci Directorate, Frederick, MD USA.
-
- Shen, Tsai-Wei (author)
- Frederick Natl Lab Canc Res, Adv Biomed & Computat Sci, Biomed Informat & Data Sci Directorate, Frederick, MD USA.
-
- Chen, Zhong (author)
- Loma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA.
-
- Stanbouly, Seta (author)
- Loma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA.
-
- Tran, Bao (author)
- Frederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA.
-
- Shetty, Jyoti (author)
- Frederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA.
-
- Kriga, Yuliya (author)
- Frederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA.
-
- Meerzaman, Daoud (author)
- NCI, Computat Genom & Bioinformat Branch, Ctr Biomed Informat & Informat Technol CBIIT, Rockville, MD USA.
-
- Nguyen, Cu (author)
- NCI, Computat Genom & Bioinformat Branch, Ctr Biomed Informat & Informat Technol CBIIT, Rockville, MD USA.
-
- Petitjean, Virginie (author)
- Novartis Inst Biomed Res, Biomarker Dev, Basel, Switzerland.
-
- Sultan, Marc (author)
- Novartis Inst Biomed Res, Biomarker Dev, Basel, Switzerland.
-
- Cam, Margaret (author)
- Ctr Canc Res, Off Sci & Technol Resources, CCR Collaborat Bioinformat Resource CCBR, Bethesda, MD USA.
-
- Mehta, Monika (author)
- Frederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA.
-
- Hung, Tiffany (author)
- Genentech Inc, San Francisco, CA 94080 USA.
-
- Peters, Eric (author)
- Genentech Inc, San Francisco, CA 94080 USA.
-
- Kalamegham, Rasika (author)
- Genentech Inc, San Francisco, CA 94080 USA.
-
- Sahraeian, Sayed Mohammad Ebrahim (author)
- Roche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA.
-
- Mohiyuddin, Marghoob (author)
- Roche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA.
-
- Guo, Yunfei (author)
- Roche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA.
-
- Yao, Lijing (author)
- Roche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA.
-
- Song, Lei (author)
- NCI, Div Canc Epidemiol & Genet, NIH, Bethesda, MD 20892 USA.
-
- Lam, Hugo Y. K. (author)
- Roche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA.
-
- Drabek, Jiri (author)
- Palacky Univ, Fac Med & Dent, IMTM, Olomouc, Czech Republic.;European Infrastruct Translat Med, Amsterdam, Netherlands.
-
- Vojta, Petr (author)
- European Infrastruct Translat Med, Amsterdam, Netherlands.;NCI, Ctr Riferimento Oncol Aviano CRO IRCCS, Unit Oncogenet & Funct Oncogen, Aviano, Italy.
-
- Maestro, Roberta (author)
- European Infrastruct Translat Med, Amsterdam, Netherlands.;NCI, Ctr Riferimento Oncol Aviano CRO IRCCS, Unit Oncogenet & Funct Oncogen, Aviano, Italy.
-
- Gasparotto, Daniela (author)
- European Infrastruct Translat Med, Amsterdam, Netherlands.;Perron Inst Neurol & Translat Sci, Nedlands, WA, Australia.;Univ Tartu, Estonian Genome Ctr, Inst Genom, Tartu, Estonia.
-
- Koks, Sulev (author)
- European Infrastruct Translat Med, Amsterdam, Netherlands.;Univ Tartu, Estonian Genome Ctr, Inst Genom, Tartu, Estonia.
-
- Reimann, Ene (author)
- European Infrastruct Translat Med, Amsterdam, Netherlands.;Univ Helsinki, Inst Mol Med Finland FIMM, Helsinki, Finland.
-
- Scherer, Andreas (author)
- European Infrastruct Translat Med, Amsterdam, Netherlands.;Uppsala Univ, Dept Med Sci, Mol Med & Sci Life Lab, Uppsala, Sweden.
-
- Nordlund, Jessica (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab,European Infrastruct Translat Med, Amsterdam, Netherlands; Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
-
- Liljedahl, Ulrika (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab,European Infrastruct Translat Med, Amsterdam, Netherlands
-
- Jensen, Roderick, V (author)
- Virginia Tech, Dept Biol Sci, Blacksburg, VA USA.
-
- Pirooznia, Mehdi (author)
- NHLBI, Bioinformat & Computat Biol Core, NIH, Bldg 10, Bethesda, MD 20892 USA.
-
- Li, Zhipan (author)
- Sentieon Inc, Mountain View, CA USA.
-
- Xiao, Chunlin (author)
- NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 10, Bethesda, MD 20892 USA.
-
- Sherry, Stephen T. (author)
- NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 10, Bethesda, MD 20892 USA.
-
- Kusko, Rebecca (author)
- Immuneering Corp, Boston, MA USA.
-
- Moos, Malcolm (author)
- US FDA, Ctr Biol Evaluat & Res, Silver Spring, MD USA.
-
- Donaldson, Eric (author)
- US FDA, Ctr Drug Evaluat & Res, Silver Spring, MD USA.
-
- Tezak, Zivana (author)
- US FDA, Ctr Devices & Radiol Hlth, Silver Spring, MD 20993 USA.
-
- Ning, Baitang (author)
- US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA.
-
- Tong, Weida (author)
- US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA.
-
- Li, Jing (author)
- Guangzhou Med Univ, Affiliated Hosp 1, Guangzhou Inst Resp Hlth,Dept Allergy & Clin Immu, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou, Peoples R China.
-
- Duerken-Hughes, Penelope (author)
- Loma Linda Univ, Sch Med, Dept Basic Sci, Loma Linda, CA 92350 USA.
-
- Catalanotti, Claudia (author)
- 10x Genom, Pleasanton, CA USA.
-
- Maheshwari, Shamoni (author)
- 10x Genom, Pleasanton, CA USA.
-
- Shuga, Joe (author)
- 10x Genom, Pleasanton, CA USA.
-
- Liang, Winnie S. (author)
- Translat Genom Res Inst, Phoenix, AZ USA.
-
- Keats, Jonathan (author)
- Translat Genom Res Inst, Phoenix, AZ USA.
-
- Adkins, Jonathan (author)
- Translat Genom Res Inst, Phoenix, AZ USA.
-
- Tassone, Erica (author)
- Translat Genom Res Inst, Phoenix, AZ USA.
-
- Zismann, Victoria (author)
- Translat Genom Res Inst, Phoenix, AZ USA.
-
- McDaniel, Timothy (author)
- Translat Genom Res Inst, Phoenix, AZ USA.
-
- Trent, Jeffrey (author)
- Translat Genom Res Inst, Phoenix, AZ USA.
-
- Foox, Jonathan (author)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY USA.
-
- Butler, Daniel (author)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY USA.
-
- Mason, Christopher E. (author)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY USA.
-
- Hong, Huixiao (author)
- US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA.
-
- Shi, Leming (author)
- Fudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China.
-
- Wang, Charles (author)
- Loma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA.;Loma Linda Univ, Sch Med, Dept Basic Sci, Loma Linda, CA 92350 USA.
-
- Xiao, Wenming (author)
- US FDA, Ctr Devices & Radiol Hlth, Silver Spring, MD 20993 USA.
-
show less...
-
Roche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA NCI, Div Canc Epidemiol & Genet, NIH, Bethesda, MD 20892 USA. (creator_code:org_t)
- 2021-09-09
- 2021
- English.
-
In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
- Related links:
-
https://www.ncbi.nlm...
-
show more...
-
https://urn.kb.se/re...
-
https://doi.org/10.1...
-
show less...
Abstract
Subject headings
Close
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
-
Fang, Li Tai
-
Zhu, Bin
-
Zhao, Yongmei
-
Chen, Wanqiu
-
Yang, Zhaowei
-
Kerrigan, Liz
-
show more...
-
Langenbach, Kurt
-
de Mars, Maryell ...
-
Lu, Charles
-
Idler, Kenneth
-
Jacob, Howard
-
Zheng, Yuanting
-
Ren, Luyao
-
Yu, Ying
-
Jaeger, Erich
-
Schroth, Gary P.
-
Abaan, Ogan D.
-
Talsania, Keyur
-
Lack, Justin
-
Shen, Tsai-Wei
-
Chen, Zhong
-
Stanbouly, Seta
-
Tran, Bao
-
Shetty, Jyoti
-
Kriga, Yuliya
-
Meerzaman, Daoud
-
Nguyen, Cu
-
Petitjean, Virgi ...
-
Sultan, Marc
-
Cam, Margaret
-
Mehta, Monika
-
Hung, Tiffany
-
Peters, Eric
-
Kalamegham, Rasi ...
-
Sahraeian, Sayed ...
-
Mohiyuddin, Marg ...
-
Guo, Yunfei
-
Yao, Lijing
-
Song, Lei
-
Lam, Hugo Y. K.
-
Drabek, Jiri
-
Vojta, Petr
-
Maestro, Roberta
-
Gasparotto, Dani ...
-
Koks, Sulev
-
Reimann, Ene
-
Scherer, Andreas
-
Nordlund, Jessic ...
-
Liljedahl, Ulrik ...
-
Jensen, Roderick ...
-
Pirooznia, Mehdi
-
Li, Zhipan
-
Xiao, Chunlin
-
Sherry, Stephen ...
-
Kusko, Rebecca
-
Moos, Malcolm
-
Donaldson, Eric
-
Tezak, Zivana
-
Ning, Baitang
-
Tong, Weida
-
Li, Jing
-
Duerken-Hughes, ...
-
Catalanotti, Cla ...
-
Maheshwari, Sham ...
-
Shuga, Joe
-
Liang, Winnie S.
-
Keats, Jonathan
-
Adkins, Jonathan
-
Tassone, Erica
-
Zismann, Victori ...
-
McDaniel, Timoth ...
-
Trent, Jeffrey
-
Foox, Jonathan
-
Butler, Daniel
-
Mason, Christoph ...
-
Hong, Huixiao
-
Shi, Leming
-
Wang, Charles
-
Xiao, Wenming
-
show less...
- About the subject
-
- MEDICAL AND HEALTH SCIENCES
-
MEDICAL AND HEAL ...
-
and Clinical Medicin ...
-
and Cancer and Oncol ...
- Articles in the publication
-
Nature Biotechno ...
- By the university
-
Uppsala University