Literature DB >> 25938371

CONSERTING: integrating copy-number analysis with structural-variation detection.

Xiang Chen1, Pankaj Gupta1, Jianmin Wang2, Joy Nakitandwe3, Kathryn Roberts4, James D Dalton4, Matthew Parker1, Samir Patel4, Linda Holmfeldt4, Debbie Payne4, John Easton5, Jing Ma3, Michael Rusch1, Gang Wu1, Aman Patel1, Suzanne J Baker6, Michael A Dyer6, Sheila Shurtleff3, Stephen Espy7, Stanley Pounds8, James R Downing3, David W Ellison3, Charles G Mullighan3, Jinghui Zhang1.   

Abstract

We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), an algorithm for detecting somatic copy-number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation on the basis of changes in read depth and the detection of localized structural variations, with high accuracy and sensitivity. Analysis of 43 cancer genomes from both pediatric and adult patients revealed novel oncogenic CNAs, complex rearrangements and subclonal CNAs missed by alternative approaches.

Entities:  

Mesh：

Substances：

Year:  2015        PMID： 25938371      PMCID： PMC4591043          DOI： 10.1038/nmeth.3394

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  24 in total

1.  Primer3 on the WWW for general users and for biologist programmers.

Authors:  S Rozen; H Skaletsky
Journal:  Methods Mol Biol       Date:  2000

2.  The Pediatric Cancer Genome Project.

Authors:  James R Downing; Richard K Wilson; Jinghui Zhang; Elaine R Mardis; Ching-Hon Pui; Li Ding; Timothy J Ley; William E Evans
Journal:  Nat Genet       Date:  2012-05-29       Impact factor: 38.330

3.  The somatic genomic landscape of glioblastoma.

Authors:  Cameron W Brennan; Roel G W Verhaak; Aaron McKenna; Benito Campos; Houtan Noushmehr; Sofie R Salama; Siyuan Zheng; Debyani Chakravarty; J Zachary Sanborn; Samuel H Berman; Rameen Beroukhim; Brady Bernard; Chang-Jiun Wu; Giannicola Genovese; Ilya Shmulevich; Jill Barnholtz-Sloan; Lihua Zou; Rahulsimham Vegesna; Sachet A Shukla; Giovanni Ciriello; W K Yung; Wei Zhang; Carrie Sougnez; Tom Mikkelsen; Kenneth Aldape; Darell D Bigner; Erwin G Van Meir; Michael Prados; Andrew Sloan; Keith L Black; Jennifer Eschbacher; Gaetano Finocchiaro; William Friedman; David W Andrews; Abhijit Guha; Mary Iacocca; Brian P O'Neill; Greg Foltz; Jerome Myers; Daniel J Weisenberger; Robert Penny; Raju Kucherlapati; Charles M Perou; D Neil Hayes; Richard Gibbs; Marco Marra; Gordon B Mills; Eric Lander; Paul Spellman; Richard Wilson; Chris Sander; John Weinstein; Matthew Meyerson; Stacey Gabriel; Peter W Laird; David Haussler; Gad Getz; Lynda Chin
Journal:  Cell       Date:  2013-10-10       Impact factor: 41.582

4.  Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia.

Authors:  Kathryn G Roberts; Ryan D Morin; Jinghui Zhang; Martin Hirst; Yongjun Zhao; Xiaoping Su; Shann-Ching Chen; Debbie Payne-Turner; Michelle L Churchman; Richard C Harvey; Xiang Chen; Corynn Kasap; Chunhua Yan; Jared Becksfort; Richard P Finney; David T Teachey; Shannon L Maude; Kane Tse; Richard Moore; Steven Jones; Karen Mungall; Inanc Birol; Michael N Edmonson; Ying Hu; Kenneth E Buetow; I-Ming Chen; William L Carroll; Lei Wei; Jing Ma; Maria Kleppe; Ross L Levine; Guillermo Garcia-Manero; Eric Larsen; Neil P Shah; Meenakshi Devidas; Gregory Reaman; Malcolm Smith; Steven W Paugh; William E Evans; Stephan A Grupp; Sima Jeha; Ching-Hon Pui; Daniela S Gerhard; James R Downing; Cheryl L Willman; Mignon Loh; Stephen P Hunger; Marco A Marra; Charles G Mullighan
Journal:  Cancer Cell       Date:  2012-08-14       Impact factor: 31.743

5.  The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.

Authors:  Jinghui Zhang; Li Ding; Linda Holmfeldt; Gang Wu; Sue L Heatley; Debbie Payne-Turner; John Easton; Xiang Chen; Jianmin Wang; Michael Rusch; Charles Lu; Shann-Ching Chen; Lei Wei; J Racquel Collins-Underwood; Jing Ma; Kathryn G Roberts; Stanley B Pounds; Anatoly Ulyanov; Jared Becksfort; Pankaj Gupta; Robert Huether; Richard W Kriwacki; Matthew Parker; Daniel J McGoldrick; David Zhao; Daniel Alford; Stephen Espy; Kiran Chand Bobba; Guangchun Song; Deqing Pei; Cheng Cheng; Stefan Roberts; Michael I Barbato; Dario Campana; Elaine Coustan-Smith; Sheila A Shurtleff; Susana C Raimondi; Maria Kleppe; Jan Cools; Kristin A Shimano; Michelle L Hermiston; Sergei Doulatov; Kolja Eppert; Elisa Laurenti; Faiyaz Notta; John E Dick; Giuseppe Basso; Stephen P Hunger; Mignon L Loh; Meenakshi Devidas; Brent Wood; Stuart Winter; Kimberley P Dunsmore; Robert S Fulton; Lucinda L Fulton; Xin Hong; Christopher C Harris; David J Dooling; Kerri Ochoa; Kimberly J Johnson; John C Obenauer; William E Evans; Ching-Hon Pui; Clayton W Naeve; Timothy J Ley; Elaine R Mardis; Richard K Wilson; James R Downing; Charles G Mullighan
Journal:  Nature       Date:  2012-01-11       Impact factor: 49.962

6.  A novel retinoblastoma therapy from genomic and epigenetic analyses.

Authors:  Jinghui Zhang; Claudia A Benavente; Justina McEvoy; Jacqueline Flores-Otero; Li Ding; Xiang Chen; Anatoly Ulyanov; Gang Wu; Matthew Wilson; Jianmin Wang; Rachel Brennan; Michael Rusch; Amity L Manning; Jing Ma; John Easton; Sheila Shurtleff; Charles Mullighan; Stanley Pounds; Suraj Mukatira; Pankaj Gupta; Geoff Neale; David Zhao; Charles Lu; Robert S Fulton; Lucinda L Fulton; Xin Hong; David J Dooling; Kerri Ochoa; Clayton Naeve; Nicholas J Dyson; Elaine R Mardis; Armita Bahrami; David Ellison; Richard K Wilson; James R Downing; Michael A Dyer
Journal:  Nature       Date:  2012-01-11       Impact factor: 49.962

7.  Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.

Authors:  J Zachary Sanborn; Sofie R Salama; Mia Grifford; Cameron W Brennan; Tom Mikkelsen; Suresh Jhanwar; Sol Katzman; Lynda Chin; David Haussler
Journal:  Cancer Res       Date:  2013-08-12       Impact factor: 12.701

8.  Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas.

Authors:  Jinghui Zhang; Gang Wu; Claudia P Miller; Ruth G Tatevossian; James D Dalton; Bo Tang; Wilda Orisme; Chandanamali Punchihewa; Matthew Parker; Ibrahim Qaddoumi; Fredrick A Boop; Charles Lu; Cyriac Kandoth; Li Ding; Ryan Lee; Robert Huether; Xiang Chen; Erin Hedlund; Panduka Nagahawatte; Michael Rusch; Kristy Boggs; Jinjun Cheng; Jared Becksfort; Jing Ma; Guangchun Song; Yongjin Li; Lei Wei; Jianmin Wang; Sheila Shurtleff; John Easton; David Zhao; Robert S Fulton; Lucinda L Fulton; David J Dooling; Bhavin Vadodaria; Heather L Mulder; Chunlao Tang; Kerri Ochoa; Charles G Mullighan; Amar Gajjar; Richard Kriwacki; Denise Sheer; Richard J Gilbertson; Elaine R Mardis; Richard K Wilson; James R Downing; Suzanne J Baker; David W Ellison
Journal:  Nat Genet       Date:  2013-04-14       Impact factor: 38.330

9.  C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma.

Authors:  Matthew Parker; Kumarasamypet M Mohankumar; Chandanamali Punchihewa; Ricardo Weinlich; James D Dalton; Yongjin Li; Ryan Lee; Ruth G Tatevossian; Timothy N Phoenix; Radhika Thiruvenkatam; Elsie White; Bo Tang; Wilda Orisme; Kirti Gupta; Michael Rusch; Xiang Chen; Yuxin Li; Panduka Nagahawhatte; Erin Hedlund; David Finkelstein; Gang Wu; Sheila Shurtleff; John Easton; Kristy Boggs; Donald Yergeau; Bhavin Vadodaria; Heather L Mulder; Jared Becksfort; Jared Becksford; Pankaj Gupta; Robert Huether; Jing Ma; Guangchun Song; Amar Gajjar; Thomas Merchant; Frederick Boop; Amy A Smith; Li Ding; Charles Lu; Kerri Ochoa; David Zhao; Robert S Fulton; Lucinda L Fulton; Elaine R Mardis; Richard K Wilson; James R Downing; Douglas R Green; Jinghui Zhang; David W Ellison; Richard J Gilbertson
Journal:  Nature       Date:  2014-02-19       Impact factor: 49.962

10.  The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma.

Authors:  Gang Wu; Alexander K Diaz; Barbara S Paugh; Sherri L Rankin; Bensheng Ju; Yongjin Li; Xiaoyan Zhu; Chunxu Qu; Xiang Chen; Junyuan Zhang; John Easton; Michael Edmonson; Xiaotu Ma; Charles Lu; Panduka Nagahawatte; Erin Hedlund; Michael Rusch; Stanley Pounds; Tong Lin; Arzu Onar-Thomas; Robert Huether; Richard Kriwacki; Matthew Parker; Pankaj Gupta; Jared Becksfort; Lei Wei; Heather L Mulder; Kristy Boggs; Bhavin Vadodaria; Donald Yergeau; Jake C Russell; Kerri Ochoa; Robert S Fulton; Lucinda L Fulton; Chris Jones; Frederick A Boop; Alberto Broniscer; Cynthia Wetmore; Amar Gajjar; Li Ding; Elaine R Mardis; Richard K Wilson; Michael R Taylor; James R Downing; David W Ellison; Jinghui Zhang; Suzanne J Baker
Journal:  Nat Genet       Date:  2014-04-06       Impact factor: 38.330
View more
  40 in total

1.  Germline deletion of ETV6 in familial acute lymphoblastic leukemia.

Authors:  Evadnie Rampersaud; David S Ziegler; Ilaria Iacobucci; Debbie Payne-Turner; Michelle L Churchman; Kasmintan A Schrader; Vijai Joseph; Kenneth Offit; Katherine Tucker; Rosemary Sutton; Meera Warby; Georgia Chenevix-Trench; David G Huntsman; Maria Tsoli; R Scott Mead; Chunxu Qu; Vasiliki Leventaki; Gang Wu; Charles G Mullighan
Journal:  Blood Adv       Date:  2019-04-09

2.  Germline Genetic IKZF1 Variation and Predisposition to Childhood Acute Lymphoblastic Leukemia.

Authors:  Michelle L Churchman; Maoxiang Qian; Geertruy Te Kronnie; Ranran Zhang; Wenjian Yang; Hui Zhang; Tobia Lana; Paige Tedrick; Rebekah Baskin; Katherine Verbist; Jennifer L Peters; Meenakshi Devidas; Eric Larsen; Ian M Moore; Zhaohui Gu; Chunxu Qu; Hiroki Yoshihara; Shaina N Porter; Shondra M Pruett-Miller; Gang Wu; Elizabeth Raetz; Paul L Martin; W Paul Bowman; Naomi Winick; Elaine Mardis; Robert Fulton; Martin Stanulla; William E Evans; Mary V Relling; Ching-Hon Pui; Stephen P Hunger; Mignon L Loh; Rupert Handgretinger; Kim E Nichols; Jun J Yang; Charles G Mullighan
Journal:  Cancer Cell       Date:  2018-04-19       Impact factor: 31.743

3.  The genomic landscape of core-binding factor acute myeloid leukemias.

Authors:  Zachary J Faber; Xiang Chen; Amanda Larson Gedman; Kristy Boggs; Jinjun Cheng; Jing Ma; Ina Radtke; Jyh-Rong Chao; Michael P Walsh; Guangchun Song; Anna K Andersson; Jinjun Dang; Li Dong; Yu Liu; Robert Huether; Zhongling Cai; Heather Mulder; Gang Wu; Michael Edmonson; Michael Rusch; Chunxu Qu; Yongjin Li; Bhavin Vadodaria; Jianmin Wang; Erin Hedlund; Xueyuan Cao; Donald Yergeau; Joy Nakitandwe; Stanley B Pounds; Sheila Shurtleff; Robert S Fulton; Lucinda L Fulton; John Easton; Evan Parganas; Ching-Hon Pui; Jeffrey E Rubnitz; Li Ding; Elaine R Mardis; Richard K Wilson; Tanja A Gruber; Charles G Mullighan; Richard F Schlenk; Peter Paschka; Konstanze Döhner; Hartmut Döhner; Lars Bullinger; Jinghui Zhang; Jeffery M Klco; James R Downing
Journal:  Nat Genet       Date:  2016-10-31       Impact factor: 38.330

4.  Exploring genomic alteration in pediatric cancer using ProteinPaint.

Authors:  Xin Zhou; Michael N Edmonson; Mark R Wilkinson; Aman Patel; Gang Wu; Yu Liu; Yongjin Li; Zhaojie Zhang; Michael C Rusch; Matthew Parker; Jared Becksfort; James R Downing; Jinghui Zhang
Journal:  Nat Genet       Date:  2016-01       Impact factor: 38.330

5.  Targeted Exome Sequencing Outcome Variations of Colorectal Tumors within and across Two Sequencing Platforms.

Authors:  Hassan Ashktorab; Hamed Azimi; Michael L Nickerson; Sara Bass; Sudhir Varma; Hassan Brim
Journal:  Next Gener Seq Appl       Date:  2016-03-14

6.  Comparison of genome sequencing and clinical genotyping for pharmacogenes.

Authors:  W Yang; G Wu; U Broeckel; C A Smith; V Turner; C E Haidar; S Wang; R Carter; S E Karol; G Neale; K R Crews; J J Yang; C G Mullighan; J R Downing; W E Evans; M V Relling
Journal:  Clin Pharmacol Ther       Date:  2016-08-18       Impact factor: 6.875

7.  Germline Mutations in Predisposition Genes in Pediatric Cancer.

Authors:  Jinghui Zhang; Michael F Walsh; Gang Wu; Kim E Nichols; Michael N Edmonson; Tanja A Gruber; John Easton; Dale Hedges; Xiaotu Ma; Xin Zhou; Donald A Yergeau; Mark R Wilkinson; Bhavin Vadodaria; Xiang Chen; Rose B McGee; Stacy Hines-Dowell; Regina Nuccio; Emily Quinn; Sheila A Shurtleff; Michael Rusch; Aman Patel; Jared B Becksfort; Shuoguo Wang; Meaghann S Weaver; Li Ding; Elaine R Mardis; Richard K Wilson; Amar Gajjar; David W Ellison; Alberto S Pappo; Ching-Hon Pui; James R Downing
Journal:  N Engl J Med       Date:  2015-11-18       Impact factor: 91.245

8.  Network-based systems pharmacology reveals heterogeneity in LCK and BCL2 signaling and therapeutic sensitivity of T-cell acute lymphoblastic leukemia.

Authors:  Yoshihiro Gocho; Jingjing Liu; Jianzhong Hu; Wentao Yang; Neekesh V Dharia; Jingliao Zhang; Hao Shi; Guoqing Du; August John; Ting-Nien Lin; Jeremy Hunt; Xin Huang; Bensheng Ju; Lauren Rowland; Lei Shi; Dylan Maxwell; Brandon Smart; Kristine R Crews; Wenjian Yang; Kohei Hagiwara; Yingchi Zhang; Kathryn Roberts; Hong Wang; Elias Jabbour; Wendy Stock; Bartholomew Eisfelder; Elisabeth Paietta; Scott Newman; Giovanni Roti; Mark Litzow; John Easton; Jinghui Zhang; Junmin Peng; Hongbo Chi; Stanley Pounds; Mary V Relling; Hiroto Inaba; Xiaofan Zhu; Steven Kornblau; Ching-Hon Pui; Marina Konopleva; David Teachey; Charles G Mullighan; Kimberly Stegmaier; William E Evans; Jiyang Yu; Jun J Yang
Journal:  Nat Cancer       Date:  2021-01-21

9.  Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia.

Authors:  Lindsey E Montefiori; Sonja Bendig; Zhaohui Gu; Xiaolong Chen; Petri Pölönen; Xiaotu Ma; Alex Murison; Andy Zeng; Laura Garcia-Prat; Kirsten Dickerson; Ilaria Iacobucci; Sherif Abdelhamed; Ryan Hiltenbrand; Paul E Mead; Cyrus M Mehr; Beisi Xu; Zhongshan Cheng; Ti-Cheng Chang; Tamara Westover; Jing Ma; Anna Stengel; Shunsuke Kimura; Chunxu Qu; Marcus B Valentine; Marissa Rashkovan; Selina Luger; Mark R Litzow; Jacob M Rowe; Monique L den Boer; Victoria Wang; Jun Yin; Steven M Kornblau; Stephen P Hunger; Mignon L Loh; Ching-Hon Pui; Wenjian Yang; Kristine R Crews; Kathryn G Roberts; Jun J Yang; Mary V Relling; William E Evans; Wendy Stock; Elisabeth M Paietta; Adolfo A Ferrando; Jinghui Zhang; Wolfgang Kern; Torsten Haferlach; Gang Wu; John E Dick; Jeffery M Klco; Claudia Haferlach; Charles G Mullighan
Journal:  Cancer Discov       Date:  2021-06-08       Impact factor: 39.397

10.  Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing.

Authors:  Scott Newman; Joy Nakitandwe; Chimene A Kesserwan; Elizabeth M Azzato; David A Wheeler; David W Ellison; James R Downing; Jinghui Zhang; Kim E Nichols; Michael Rusch; Sheila Shurtleff; Dale J Hedges; Kayla V Hamilton; Scott G Foy; Michael N Edmonson; Andrew Thrasher; Armita Bahrami; Brent A Orr; Jeffery M Klco; Jiali Gu; Lynn W Harrison; Lu Wang; Michael R Clay; Annastasia Ouma; Antonina Silkov; Yanling Liu; Zhaojie Zhang; Yu Liu; Samuel W Brady; Xin Zhou; Ti-Cheng Chang; Manjusha Pande; Eric Davis; Jared Becksfort; Aman Patel; Mark R Wilkinson; Delaram Rahbarinia; Manish Kubal; Jamie L Maciaszek; Victor Pastor; Jay Knight; Alexander M Gout; Jian Wang; Zhaohui Gu; Charles G Mullighan; Rose B McGee; Emily A Quinn; Regina Nuccio; Roya Mostafavi; Elsie L Gerhardt; Leslie M Taylor; Jessica M Valdez; Stacy J Hines-Dowell; Alberto S Pappo; Giles Robinson; Liza-Marie Johnson; Ching-Hon Pui
Journal:  Cancer Discov       Date:  2021-12-01       Impact factor: 39.397
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.