Pubfacts - Scientific Publication Data
  • Categories
  • |
  • Journals
  • |
  • Authors
  • Login
  • Categories
  • Journals

Search Our Scientific Publications & Authors

Publications
  • Publications
  • Authors
find publications by category +
Translate page:

3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets.

Authors:
Jianjiong Gao Matthew T Chang Hannah C Johnsen Sizhi Paul Gao Brooke E Sylvester Selcuk Onur Sumer Hongxin Zhang David B Solit Barry S Taylor Nikolaus Schultz Chris Sander

Genome Med 2017 01 23;9(1). Epub 2017 Jan 23.

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

Many mutations in cancer are of unknown functional significance. Standard methods use statistically significant recurrence of mutations in tumor samples as an indicator of functional impact. We extend such analyses into the long tail of rare mutations by considering recurrence of mutations in clusters of spatially close residues in protein structures. Analyzing 10,000 tumor exomes, we identify more than 3000 rarely mutated residues in proteins as potentially functional and experimentally validate several in RAC1 and MAP2K1. These potential driver mutations (web resources: 3dhotspots.org and cBioPortal.org) can extend the scope of genomically informed clinical trials and of personalized choice of therapy.

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-016-0393-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5260099PMC
January 2017

Publication Analysis

Top Keywords

recurrence mutations
8
rare mutations
8
mutations cancer
8
mutations
7
cbioportalorg extend
4
clusters spatially
4
spatially close
4
structures analyzing
4
close residues
4
3dhotspotsorg cbioportalorg
4
residues protein
4
protein structures
4
considering recurrence
4
analyses long
4
scope genomically
4
rac1 map2k1
4
long tail
4
tail rare
4
resources 3dhotspotsorg
4
mutations considering
4

Altmetric Statistics


Show full details
115 Total Shares
1 Google+ Users
99 Tweets
100 Citations

Similar Publications

Past medical history of tumors other than meningioma is a negative prognostic factor for tumor recurrence in meningiomas WHO grade I.

Authors:
Annamaria Biczok Philipp Karschnia Raffaela Vitalini Markus Lenski Tobias Greve Jun Thorsteinsdottir Rupert Egensperger Franziska Dorn Jörg-Christian Tonn Christian Schichor

Acta Neurochir (Wien) 2021 Mar 5. Epub 2021 Mar 5.

Department of Neurosurgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, 81377, Munich, Germany.

Background: Prognostic markers for meningioma recurrence are needed to guide patient management. Apart from rare hereditary syndromes, the impact of a previous unrelated tumor disease on meningioma recurrence has not been described before.

Methods: We retrospectively searched our database for patients with meningioma WHO grade I and complete resection provided between 2002 and 2016. Read More

View Article and Full-Text PDF
March 2021
Similar Publications

Type and Gene Location of Mutations Predict Progression-Free Survival to First-Line Imatinib in Gastrointestinal Stromal Tumors: A Look into the Exon.

Authors:
Lorena Incorvaia Daniele Fanale Bruno Vincenzi Ida De Luca Tommaso Vincenzo Bartolotta Roberto Cannella Gianni Pantuso Daniela Cabibi Antonio Russo Viviana Bazan Giuseppe Badalamenti

Cancers (Basel) 2021 Feb 27;13(5). Epub 2021 Feb 27.

Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy.

In previous studies on localized GISTs, exon 11 deletions and mutations involving codons 557/558 showed an adverse prognostic influence on recurrence-free survival. In the metastatic setting, there are limited data on how mutation type and codon location might contribute to progression-free survival (PFS) variability to first-line imatinib treatment. We analyzed the type and gene location of and mutations for 206 patients from a GIST System database prospectively collected at an Italian reference center between January 2005 and September 2020. Read More

View Article and Full-Text PDF
February 2021
Similar Publications

Clinical Perspectives in Addressing Unsolved Issues in (Neo)Adjuvant Therapy for Primary Breast Cancer.

Authors:
Ryungsa Kim Takanori Kin

Cancers (Basel) 2021 Feb 23;13(4). Epub 2021 Feb 23.

Department of Breast Surgery, Hiroshima City Hospital, 7-33, Moto-machi, Naka-ku, Hiroshima 730-8518, Japan.

The treatment of primary breast cancer has evolved over the past 50 years based on the concept that breast cancer is a systemic disease, with the escalation of adjuvant and neoadjuvant therapies and de-escalation of breast cancer surgery. Despite the development of these therapies, recurrence with distant metastasis during the 10 years after surgical treatment is observed, albeit infrequently. Recent advances in genomic analysis based on circulating tumor cells and circulating tumor DNA have enabled the development of targeted therapies based on genetic mutations in residual tumor cells. Read More

View Article and Full-Text PDF
February 2021
Similar Publications

Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting and Uncovers a Treatment-Related Mutational Signature.

Authors:
Helen R Davies Kevin D Broad Zerrin Onadim Elizabeth A Price Xueqing Zou Ibrahim Sheriff Esin Kotiloğlu Karaa Irene Scheimberg M Ashwin Reddy Mandeep S Sagoo Shin-Ichi Ohnuma Serena Nik-Zainal

Cancers (Basel) 2021 Feb 11;13(4). Epub 2021 Feb 11.

Academic Department of Medical Genetics, University of Cambridge, Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.

The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the gene. However, cases exist where mutations are undetectable, suggesting alternative pathways to malignancy. We used whole-genome sequencing (WGS) and transcriptomics to investigate the landscape of sporadic retinoblastomas derived from twenty patients, sought and other driver mutations and investigated mutational signatures. Read More

View Article and Full-Text PDF
February 2021
Similar Publications

Molecular Profiling of 22 Primary Atypical Meningiomas Shows the Prognostic Significance of 18q Heterozygous Loss and Homozygous Deletion on Recurrence-Free Survival.

Authors:
Valeria Barresi Michele Simbolo Adele Fioravanzo Maria Liliana Piredda Maria Caffo Claudio Ghimenton Giampietro Pinna Michele Longhi Antonio Nicolato Aldo Scarpa

Cancers (Basel) 2021 Feb 21;13(4). Epub 2021 Feb 21.

Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy.

The use of adjuvant therapy is controversial in atypical meningiomas with gross total resection. Predictors of recurrence risk could be useful in selecting patients for additional treatments. The aim of this study was to investigate whether molecular features are associated with recurrence risk of atypical meningiomas. Read More

View Article and Full-Text PDF
February 2021
Similar Publications
© 2021 PubFacts.
  • About PubFacts
  • Privacy Policy
  • Sitemap