NDLI: Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models

Content Provider	Springer Nature : BioMed Central
Author	Deng, Niantao Minoche, Andre Harvey, Kate Li, Meng Winkler, Juliane Goga, Andrei Swarbrick, Alex
Abstract	Background Breast cancer cell lines (BCCLs) and patient-derived xenografts (PDXs) are the most frequently used models in breast cancer research. Despite their widespread usage, genome sequencing of these models is incomplete, with previous studies only focusing on targeted gene panels, whole exome or shallow whole genome sequencing. Deep whole genome sequencing is the most sensitive and accurate method to detect single nucleotide variants and indels, gene copy number and structural events such as gene fusions. Results Here we describe deep whole genome sequencing (WGS) of commonly used BCCL and PDX models using the Illumina X10 platform with an average ~ 60 × coverage. We identify novel genomic alterations, including point mutations and genomic rearrangements at base-pair resolution, compared to previously available sequencing data. Through integrative analysis with publicly available functional screening data, we annotate new genomic features likely to be of biological significance. CSMD1, previously identified as a tumor suppressor gene in various cancer types, including head and neck, lung and breast cancers, has been identified with deletion in 50% of our PDX models, suggesting an important role in aggressive breast cancers. Conclusions Our WGS data provides a comprehensive genome sequencing resource of these models.
Related Links	https://breast-cancer-research.biomedcentral.com/counter/pdf/10.1186/s13058-022-01540-0.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
DOI	10.1186/s13058-022-01540-0
Journal	Breast Cancer Research
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2022-09-24
Access Restriction	Open
Subject Keyword	Cancer Research Oncology Surgical Oncology Breast cancer cell lines Patient-derived xenografts Whole genome sequencing Structural variants Non-coding mutations
Content Type	Text
Resource Type	Article
Subject	Cancer Research Oncology
Journal Impact Factor	6.1/2023
5-Year Journal Impact Factor	7.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

New generation breast cancer cell lines developed from patient-derived xenografts

Molecular profiling of patient-derived breast cancer xenografts

Factors associated with engraftment success of patient-derived xenografts of breast cancer

Genomic profile of metastatic breast cancer patient-derived xenografts established using percutaneous biopsy

Know thy cells: commonly used triple-negative human breast cancer cell lines carry mutations in RAS and effectors

Patient-derived breast tumor xenografts facilitating personalized cancer therapy

Genetic Profiles Associated with Chemoresistance in Patient-Derived Xenograft Models of Ovarian Cancer.

Establishing Patient-Derived Cancer Cell Cultures and Xenografts in Biliary Tract Cancer.

Genomic and Molecular Signatures of Successful Patient-Derived Xenografts for Oral Cavity Squamous Cell Carcinoma

Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models

Similar Documents

New generation breast cancer cell lines developed from patient-derived xenografts

Molecular profiling of patient-derived breast cancer xenografts

Factors associated with engraftment success of patient-derived xenografts of breast cancer

Genomic profile of metastatic breast cancer patient-derived xenografts established using percutaneous biopsy

Know thy cells: commonly used triple-negative human breast cancer cell lines carry mutations in RAS and effectors

Patient-derived breast tumor xenografts facilitating personalized cancer therapy

Genetic Profiles Associated with Chemoresistance in Patient-Derived Xenograft Models of Ovarian Cancer.

Establishing Patient-Derived Cancer Cell Cultures and Xenografts in Biliary Tract Cancer.

Genomic and Molecular Signatures of Successful Patient-Derived Xenografts for Oral Cavity Squamous Cell Carcinoma

Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models