Genomics in the Scientific Literature: Cancer

Genomics in the Scientific Literature
Topics in the Scientific Literature

Cancer
1. Cardiovascular DiseaseChronic DiseaseEpigenomicsEthical, Legal, and Social Issues (ELSI)Genetic TestingNeurologic ConditionsPersonalized MedicineOtherHuGECancer
A systematic review of the relationship between polymorphic sites in the estrogen receptor-beta (ESR2) gene and breast cancer risk
Yu KD, et al.
Breast Cancer Res Treat 2010 Apr

Breast Cancer Res Treat. 2010 Apr 14. [Epub ahead of print]

A systematic review of the relationship between polymorphic sites in the estrogen receptor-beta (ESR2) gene and breast cancer risk.
Yu KD, Rao NY, Chen AX, Fan L, Yang C, Shao ZM.

Department of Breast Surgery, Cancer Hospital/Cancer Institute, Breast Cancer Institute, Fudan University, 399 Ling-Ling Road, 200032, Shanghai, People's Republic of China.

Abstract
The estrogen signal is mediated by the estrogen receptor (ER). The specific role of ER-beta, a second ER, in breast carcinogenesis is not known. A number of association studies have been carried out to investigate the relationship between polymorphic sites in the ESR2 gene and breast cancer risk, however, the results are inconsistent. We searched PubMed, Medline, and Web of Science database (updated to 10 January 2010) and identified 13 relevant case-control studies, and approximately 28 single-nucleotide polymorphisms (SNPs) and one micro-satellite marker were reported in the literature. The median number of study subjects was 776 (range 158-13,550). Three genetic variants [(CA)n, rs2987983, and rs4986938] showed significant overall associations with breast cancer, and rs4986938 was reported twice. Because rs4986938 and rs1256049 were the most extensively studied polymorphisms, we subsequently conducted a meta-analysis to evaluate their relationship with breast cancer risk (9 studies of 10,837 cases and 16,021 controls for rs4986938; 8 studies of 11,652 cases and 15,726 controls for rs1256049). For rs4986938, the women harboring variant allele seemed to be associated with a decreased risk either in the dominant model [pooled OR = 0.944, 95% confidence interval (95% CI) 0.897-0.993, fixed-effects] or in the co-dominant model (AG vs. GG) (OR = 0.944, 95% CI 0.895-0.997, fixed-effects). rs1256049 was not associated with breast cancer risk in any model. Five studies had investigated the effect of haplotypes in the ESR2 gene on breast cancer risk, and four of them had positive outcomes. In summary, the present systematic review suggests that SNP rs4986938 as well as haplotypes in the ESR2 gene might be associated with breast cancer. The need for additional studies examining these issues seems of vital importance.

PMID: 20390341 [PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/20390341?dopt=Abstract


2. Common genetic variants and cancer risk in Mendelian cancer syndromes
Antoniou AC & Chenevix-Trench G
Curr Opin Genet Dev 2010 Apr

Curr Opin Genet Dev. 2010 Apr 15. [Epub ahead of print]

Common genetic variants and cancer risk in Mendelian cancer syndromes.
Antoniou AC, Chenevix-Trench G.

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK.

Abstract
Multiple lines of evidence suggest that genetic factors modify the cancer risks in carriers of mutations in Mendelian cancer syndromes. We review the latest evidence for genetic modifiers of risk for four Mendelian cancer syndromes. In general, candidate gene studies have not been very successful at identifying modifier genes and most studies have been underpowered, but recently polymorphisms identified through genome wide association studies of unselected cancer patients and controls have been shown to modify cancer risk in studies of large numbers of mutation carriers. This approach has identified two genetic variants that are associated with colorectal cancer risk in Lynch Syndrome, and five polymorphisms that are associated with the risk of breast cancer for BRCA1 and/or BRCA2 mutation carriers. As predicted from the association between these five polymorphisms and risk of estrogen-positive or estrogen-negative breast cancer in the general population, differential associations of these polymorphisms with breast cancer risk were found for BRCA1 and BRCA2 mutation carriers presumably because BRCA1 breast cancer tumors are predominantly ER-negative and are biologically distinct from BRCA2 breast cancers. These findings suggest that studies of mutation carriers may be useful for identifying genetic variants associated with different disease subtypes. The current literature underlies the need for increased international collaboration between individual studies, and the continued recruitment of mutation carriers, in order to reliably estimate and identify the genetic modifiers of risk in Mendelian cancer syndromes. Copyright © 2010 Elsevier Ltd. All rights reserved.

PMID: 20399636 [PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/20399636?dopt=Abstract


3. Genetic and familial factors influencing breast, colon, prostate and lung cancers
Stein QP & Flanagan JD
S D Med 2010;Spec No:16-22

S D Med. 2010;Spec No:16-22.

Genetic and familial factors influencing breast, colon, prostate and lung cancers.
Stein QP, Flanagan JD.

Sanford Women's Health & Sanford Children's Specialty Clinic, South Dakota, USA.

Abstract
Knowledge of cancer genetics is advancing our biological understanding of breast, colon, prostate and lung cancers. A family history of any one of these four types of cancer can increase an individual's personal risk to also develop a malignancy. For some families, genetic testing, in combination with genetic counseling, can be a helpful way to identify a hereditary cancer predisposition gene or establish a cancer risk management plan. In this paper, we will review the current state of knowledge surrounding genetic factors influencing breast, colon, prostate and lung cancer.

PMID: 20397487 [PubMed - in process]
http://www.ncbi.nlm.nih.gov/pubmed/20397487?dopt=Abstract


4. HER2 Ile655Val polymorphism contributes to breast cancer risk: evidence from 27 case-control studies
Lu S, et al.
Breast Cancer Res Treat 2010 Apr

Breast Cancer Res Treat. 2010 Apr 17. [Epub ahead of print]

HER2 Ile655Val polymorphism contributes to breast cancer risk: evidence from 27 case-control studies.
Lu S, Wang Z, Liu H, Hao X.

Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 30006, Tianjin, China.

Abstract
Proto-oncogene HER2 (also known as erbB-2 or neu) plays an important role in the carcinogenesis and the prognosis of breast cancer. Many epidemiological studies have been conducted to explore the association between the HER2 Ile655Val polymorphism and breast cancer risk. However, inconsistency existed in the results. Therefore, we performed a meta-analysis of 27 published case-control studies including 11,504 cases and 12,538 controls. We assessed the strength of the association by crude odds ratios (ORs) with 95% confidence intervals (CIs) and reached a result that HER2 Ile655Val polymorphism was associated with an increased breast cancer risk in overall populations (for Ile/Val vs. Ile/Ile: OR = 1.05, 95% CI = 1.00-1.12, P = 0.07 for heterogeneity; for the dominant model Ile/Val + Val/Val vs. Ile/Ile: OR = 1.10, 95% CI = 1.01-1.20, P = 0.01 for heterogeneity). In subgroup analysis by ethnicity, we found a significant association among Africans (for Val/Val vs. Ile/Ile: OR = 8.78, 95% CI = 1.94-39.72, P = 0.35 for heterogeneity; for the recessive model Val/Val vs. Ile/Val +Ile/Ile: OR = 8.60, 95% CI = 1.92-38.48, P = 0.31 for heterogeneity) and Asians (for Ile/Val vs. Ile/Ile: OR = 1.18, 95% CI = 1.01-1.39, P = 0.41 for heterogeneity; for the dominant model Val/Val + Ile/Val vs. Ile/Ile: OR = 1.18, 95% CI = 1.01-1.38, P = 0.27 for heterogeneity). In conclusion, our meta-analysis suggests that HER2 Ile 655Val polymorphism may contribute to breast cancer risk.

PMID: 20401632 [PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/20401632?dopt=Abstract


5. International network of cancer genome projects
Nature 2010 Apr;464(7291):993-8

Nature. 2010 Apr 15;464(7291):993-8.

International network of cancer genome projects.
International Cancer Genome Consortium.

Collaborators (412)Hudson TJ, Anderson W, Aretz A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusuda J, Lane DP, Laplace F, Lu Y, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Bowtell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cross A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BA, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevad L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thomas G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RT, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusuda J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbaue H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, Easton DF, Spellman PT, Martin S, Barker AD, Chin L, Collins FS, Compton CC, Ferguson ML, Gerhard DS, Getz G, Gunter C, Guttmacher A, Guyer M, Hayes DN, Lander ES, Ozenberger B, Penny R, Peterson J, Sander C, Shaw KM, Speed TP, Spellman PT, Vockley JG, Wheeler DA, Wilson RK, Hudson TJ, Chin L, Knoppers BM, Lander ES, Lichter P, Stein LD, Stratton MR, Anderson W, Barker AD, Bell C, Bobrow M, Burke W, Collins FS, Compton CC, DePinho RA, Easton DF, Futreal PA, Gerhard DS, Green AR, Guyer M, Hamilton SR, Hubbard TJ, Kallioniemi OP, Kennedy KL, Ley TJ, Liu ET, Lu Y, Majumder P, Marra M, Ozenberger B, Peterson J, Schafer AJ, Spellman PT, Stunnenberg HG, Wainwright BJ, Wilson RK, Yang H.
Abstract
The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

PMID: 20393554 [PubMed - in process]
http://www.ncbi.nlm.nih.gov/pubmed/20393554?dopt=Abstract