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Article: Genomic approaches to identifying breast cancer susceptibility factors.

Struewing, Jeffery P

2004 Volume 19, Page(s) 3–9

Abstract: The majority of the genetic variants underlying susceptibility to breast cancer are yet to be discovered. Genome-wide linkage analyses, utilizing anonymous genetic markers, have been successful at identifying two genes, BRCA1 and BRCA2, which account for ...

Abstract	The majority of the genetic variants underlying susceptibility to breast cancer are yet to be discovered. Genome-wide linkage analyses, utilizing anonymous genetic markers, have been successful at identifying two genes, BRCA1 and BRCA2, which account for a sizeable fraction of the clearly inherited forms of breast cancer occurring in autosomal dominant Mendellian patterns. Mutations in these genes, however, account for less than (1/4) of the total genetic component of breast cancer susceptibility and the remaining component is likely to be polygenic in nature - the interaction of mutations in multiple genes, each with a weak effect, in combination with environmental influences. The identification of these polygenes will likely require the study of large numbers of unrelated subjects with and without breast cancer in case-control association studies. Until the time when complete genome sequence information is feasible for all study subjects, interim strategies involving a subset of all common genetic variation (primarily single nucleotide polymorphisms, SNPs) are being planned. Assuming the common disease-common variant theory of complex disease susceptibility, studying a very dense set of genetic markers is likely to identify breast cancer susceptibility genes by virtue of including either the biologically relevant variant, or one closely correlated with it due to linkage disequilibrium.
Language	English
Publishing date	2004-05-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	639267-2
ISSN	0888-6008
ISSN	0888-6008
DOI	10.3233/bd-2004-19102
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Article ; Online: Use of Next-Generation Sequencing Tests to Guide Cancer Treatment: Results From a Nationally Representative Survey of Oncologists in the United States.

JCO precision oncology

2022 Volume 2, Page(s) 1–13

Abstract: Purpose: There are no nationally representative data on oncologists' use of next-generation sequencing (NGS) testing in practice. The purpose of this study was to investigate how oncologists in the United States use NGS tests to evaluate patients with ... ...

Abstract	Purpose: There are no nationally representative data on oncologists' use of next-generation sequencing (NGS) testing in practice. The purpose of this study was to investigate how oncologists in the United States use NGS tests to evaluate patients with cancer and to inform treatment recommendations. Methods: The study used data from the National Survey of Precision Medicine in Cancer Treatment, which was mailed to a nationally representative sample of oncologists in 2017 (N = 1,281; cooperation rate = 38%). Weighted percentages were calculated to describe NGS test use. Multivariable modeling was conducted to assess the association of test use with oncologist practice characteristics. Results: Overall, 75.6% of oncologists reported using NGS tests to guide treatment decisions. Of these oncologists, 34.0% used them often to guide treatment decisions for patients with advanced refractory disease, 29.1% to determine eligibility for clinical trials, and 17.5% to decide on off-label use of Food and Drug Administration-approved drugs. NGS test results informed treatment recommendations often for 26.8%, sometimes for 52.4%, and never or rarely for 20.8% of oncologists. Oncologists younger than 50 years of age, holding a faculty appointment, having genomics training, seeing more than 50 unique patients per month, and having access to a molecular tumor board were more likely to use NGS tests. Conclusion: In 2017, most oncologists in the United States were using NGS tests to guide treatment decisions for their patients. More research is needed to establish the clinical usefulness of these tests, to develop evidence-based clinical guidelines for their use in practice, and to ensure that patients who can benefit from these new technologies receive appropriate testing and treatment.
Language	English
Publishing date	2022-01-27
Publishing country	United States
Document type	Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.18.00169
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Article ; Online: Adverse drug reaction causality assessment tools for drug-induced Stevens-Johnson syndrome and toxic epidermal necrolysis: room for improvement.

Goldman, Jennifer L / Chung, Wen-Hung / Lee, Brian R / Chen, Chun-Bing / Lu, Chun-Wei / Hoetzenecker, Wolfram / Micheletti, Robert / Yasuda, Sally Usdin / Margolis, David J / Shear, Neil H / Struewing, Jeffery P / Pirmohamed, Munir

European journal of clinical pharmacology

2019 Volume 75, Issue 8, Page(s) 1135–1141

Abstract: Purpose: Establishment of causality between drug exposure and adverse drug reactions (ADR) is challenging even for serious ADRs such as Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN). Several causality assessment tools (CAT) exist, but ... ...

Abstract	Purpose: Establishment of causality between drug exposure and adverse drug reactions (ADR) is challenging even for serious ADRs such as Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN). Several causality assessment tools (CAT) exist, but the reliability and validity of such tools is variable. The objective of this study was to compare the reliability and validity of existing ADR CATs on SJS/TEN cases. Methods: Seven investigators completed three CAT (ALDEN, Naranjo, Liverpool) for 10 SJS/TEN cases. Each CAT categorized the causality of 30 potential drugs as definite/very probable, probable, possible, or doubtful/unlikely. An additional reviewer provided expert opinion by designating the implicated drug(s) for each case. A Kappa score was generated to compare CAT responses both by method (reliability of all 7 reviewers, by CATs) and by reviewer (reliability of the 3 CAT, by reviewer). A c statistic was calculated to assess validity. Results: Inter-rater reliability by CAT was poor to fair: ALDEN 0.22, Naranjo 0.11, and Liverpool 0.12. Reliability was highest when causality classification was definite/very probable (0.16-0.41). Similarly, intra-rater reliability by reviewer was poor. When comparing the validity of the overall CAT to expert reviewer, area under the curve was highest for ALDEN (c statistic 0.65) as compared to Liverpool (0.55) or Naranjo (0.54). Conclusion: Available CAT have poor reliability and validity for drug-induced SJS/TEN. Due to the importance of determining ADR causality for research, industry, and regulatory purposes, development of an enhanced tool that can incorporate data from immunological testing and pharmacogenetic results may strengthen CAT usefulness and applicability for drug-induced SJS/TEN.
MeSH term(s)	Algorithms ; Causality ; Humans ; Pharmacovigilance ; Probability ; Reproducibility of Results ; Risk Assessment/methods ; Risk Factors ; Stevens-Johnson Syndrome/diagnosis ; Stevens-Johnson Syndrome/epidemiology ; Stevens-Johnson Syndrome/etiology
Language	English
Publishing date	2019-03-27
Publishing country	Germany
Document type	Comparative Study ; Journal Article
ZDB-ID	121960-1
ISSN	1432-1041 ; 0031-6970
ISSN (online)	1432-1041
ISSN	0031-6970
DOI	10.1007/s00228-019-02670-9
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Article ; Online: Correction to: Adverse drug reaction causality assessment tools for drug-induced Stevens-Johnson syndrome and toxic epidermal necrolysis: room for improvement.

European journal of clinical pharmacology

2019 Volume 75, Issue 9, Page(s) 1331

Abstract: The correct name of the 9th Author is David J. Margolis. The original article was corrected. ...

Abstract	The correct name of the 9th Author is David J. Margolis. The original article was corrected.
Language	English
Publishing date	2019-07-04
Publishing country	Germany
Document type	Journal Article ; Published Erratum
ZDB-ID	121960-1
ISSN	1432-1041 ; 0031-6970
ISSN (online)	1432-1041
ISSN	0031-6970
DOI	10.1007/s00228-019-02710-4
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Article: Segregation analysis of 231 Ashkenazi Jewish families for evidence of additional breast cancer susceptibility genes.

Kaufman, David J / Beaty, Terri H / Struewing, Jeffery P

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

2003 Volume 12, Issue 10, Page(s) 1045–1052

Abstract: Between 5 and 10% of breast cancer is attributable to inherited cancer susceptibility genes. Mutations in the genes BRCA1 and BRCA2 account for two-thirds of hereditary breast cancer cases. Using segregation analysis, families of cases without BRCA1/2 ... ...

Abstract	Between 5 and 10% of breast cancer is attributable to inherited cancer susceptibility genes. Mutations in the genes BRCA1 and BRCA2 account for two-thirds of hereditary breast cancer cases. Using segregation analysis, families of cases without BRCA1/2 mutations were studied for statistical evidence of another major breast cancer gene in a community-based sample of Jewish probands tested previously for the presence of three BRCA founder mutations. A total of 231 probands with breast cancer, who do not carry a founder mutation, reported complete data on 602 female first-degree relatives of probands over age 20; 78 of these relatives had breast cancer. Segregation analysis was used to evaluate the likelihood of various genetic and nongenetic models. Sporadic, environmental, and general Mendelian genetic models fit the family data poorly and were rejected. A Mendelian recessive model fit better than dominant and codominant models, although none of these could be rejected. Cumulative incidence curves predicted by the recessive and codominant models fit observed incidence among first-degree relatives well. The assumption of Mendelian transmission of a major recessive gene(s) is compatible with the data. The recessive model predicts that 4% of women would carry the high-risk genotype, with 85% of them developing breast cancer by age 70. There was significant heterogeneity between these families and the 114 BRCA1/2 mutation-positive families from the same study population, implying that this apparent recessive effect is not because of undetected BRCA1/2 mutations. The study adds support for a major autosomal recessive component to breast cancer susceptibility.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Breast Neoplasms/ethnology ; Breast Neoplasms/genetics ; DNA Mutational Analysis ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Genes, Recessive ; Genetic Predisposition to Disease ; Humans ; Jews/genetics ; Middle Aged ; Models, Genetic ; Pedigree
Language	English
Publishing date	2003-10
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1153420-5
ISSN	1055-9965
ISSN	1055-9965
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Article: Similar prevalence of founder BRCA1 and BRCA2 mutations among Ashkenazi and non-Ashkenazi men with breast cancer: evidence from 261 cases in Israel, 1976-1999.

Chodick, Gabriel / Struewing, Jeffery P / Ron, Elaine / Rutter, Joni L / Iscovich, Jose

European journal of medical genetics

2007 Volume 51, Issue 2, Page(s) 141–147

Abstract: To evaluate the potential contribution of mutations in the BRCA1 and BRCA2 genes to male breast cancer (MBC), we expanded a previous study to screen a total of 261 Israeli men diagnosed with breast carcinoma. A total of 21 BRCA2 6174delT and 8 BRCA1 ... ...

Abstract	To evaluate the potential contribution of mutations in the BRCA1 and BRCA2 genes to male breast cancer (MBC), we expanded a previous study to screen a total of 261 Israeli men diagnosed with breast carcinoma. A total of 21 BRCA2 6174delT and 8 BRCA1 185delAG mutations were found. Similar frequencies of BRCA1 and BRCA2 mutation carriers were found among Ashkenazi (12.8%) and non-Ashkenazi Jews (9.1%). The combined prevalence of BRCA1/BRCA2 founder mutations among Ashkenazi Jewish men is slightly higher than for women, due to a higher frequency of BRCA2 mutations.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Apoptosis Regulatory Proteins ; BRCA1 Protein/genetics ; BRCA2 Protein/genetics ; Breast Neoplasms, Male/genetics ; Breast Neoplasms, Male/pathology ; Founder Effect ; Genetic Predisposition to Disease ; Genetic Testing ; Germ-Line Mutation/genetics ; Humans ; Israel ; Jews/genetics ; Male ; Middle Aged ; Prevalence ; Risk Factors
Chemical Substances	Apoptosis Regulatory Proteins ; BLID protein, human ; BRCA1 Protein ; BRCA1 protein, human ; BRCA2 Protein ; BRCA2 protein, human
Language	English
Publishing date	2007-11-22
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article
ZDB-ID	2184135-4
ISSN	1878-0849 ; 1769-7212
ISSN (online)	1878-0849
ISSN	1769-7212
DOI	10.1016/j.ejmg.2007.11.001
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Article ; Online: No evidence of excess breast cancer risk among mutation-negative women from BRCA mutation-positive families.

Korde, Larissa A / Mueller, Christine M / Loud, Jennifer T / Struewing, Jeffery P / Nichols, Kathy / Greene, Mark H / Mai, Phuong L

Breast cancer research and treatment

2010 Volume 125, Issue 1, Page(s) 169–173

Abstract: This analysis addresses risk of breast cancer among women in BRCA-positive families who test negative for the family mutation. We compared the number of prospectively diagnosed breast cancers in 395 mutation-negative women from 28 BRCA1/2-positive ... ...

Abstract	This analysis addresses risk of breast cancer among women in BRCA-positive families who test negative for the family mutation. We compared the number of prospectively diagnosed breast cancers in 395 mutation-negative women from 28 BRCA1/2-positive families to an age-, race-, and calendar time-specific expected number of breast cancers derived from the SEER 9 Cancer Registry. Study participants contributed a total of 7008.1 person-years of follow-up. The mean age at study entry was 31.3 years; mean follow-up was 17.7 years. Ten women developed breast cancer yielding an observed-to-expected ratio of 0.82 (95% CI 0.39-1.51). Adjustment for possible reduction in breast cancer risk due to oophorectomy by two different methods resulted in O/E ratios in the range of 0.80-0.99. Stratification by degree of relatedness to the nearest mutation carrier did not substantially alter these results, however, women with at least one-first degree relative with breast cancer appeared to have a slightly increased, though not statistically significant, risk of breast cancer (O/E ratio = 1.33, 95% CI 0.41-2.91). Our data suggest that breast cancer risk among mutation-negative women from BRCA1/2 mutation-positive families is similar to that observed in the general population, with a possible slight increase in risk among mutation-negative women with a family history of breast cancer in a first degree relative. Although this is the largest prospective cohort yet assembled to address this important question, the number of breast cancer events is still relatively small.
MeSH term(s)	Adult ; BRCA1 Protein/genetics ; BRCA2 Protein/genetics ; Breast Neoplasms/genetics ; Breast Neoplasms/prevention & control ; Female ; Genetic Predisposition to Disease ; Humans ; Middle Aged ; Mutation ; Odds Ratio ; Ovariectomy ; Pedigree ; Prospective Studies ; Risk Assessment ; Risk Factors ; SEER Program ; Time Factors ; United States
Chemical Substances	BRCA1 Protein ; BRCA1 protein, human ; BRCA2 Protein ; BRCA2 protein, human
Language	English
Publishing date	2010-05-11
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-010-0923-y
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Article: No evidence of excess breast cancer risk among mutation-negative women from BRCA mutation-positive families

Korde, Larissa A / Mueller, Christine M / Loud, Jennifer T / Struewing, Jeffery P / Nichols, Kathy / Greene, Mark H / Mai, Phuong L

Breast cancer research and treatment. 2011 Jan., v. 125, no. 1

2011

Abstract	This analysis addresses risk of breast cancer among women in BRCA-positive families who test negative for the family mutation. We compared the number of prospectively diagnosed breast cancers in 395 mutation-negative women from 28 BRCA1/2-positive families to an age-, race-, and calendar time-specific expected number of breast cancers derived from the SEER 9 Cancer Registry. Study participants contributed a total of 7008.1 person-years of follow-up. The mean age at study entry was 31.3 years; mean follow-up was 17.7 years. Ten women developed breast cancer yielding an observed-to-expected ratio of 0.82 (95% CI 0.39-1.51). Adjustment for possible reduction in breast cancer risk due to oophorectomy by two different methods resulted in O/E ratios in the range of 0.80-0.99. Stratification by degree of relatedness to the nearest mutation carrier did not substantially alter these results, however, women with at least one-first degree relative with breast cancer appeared to have a slightly increased, though not statistically significant, risk of breast cancer (O/E ratio = 1.33, 95% CI 0.41-2.91). Our data suggest that breast cancer risk among mutation-negative women from BRCA1/2 mutation-positive families is similar to that observed in the general population, with a possible slight increase in risk among mutation-negative women with a family history of breast cancer in a first degree relative. Although this is the largest prospective cohort yet assembled to address this important question, the number of breast cancer events is still relatively small.
Language	English
Dates of publication	2011-01
Size	p. 169-173.
Publisher	Springer US
Publishing place	Boston
Document type	Article
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-010-0923-y
Database	NAL-Catalogue (AGRICOLA)

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Article: Candidate single nucleotide polymorphism selection using publicly available tools: a guide for epidemiologists.

Bhatti, Parveen / Church, Deanna M / Rutter, Joni L / Struewing, Jeffery P / Sigurdson, Alice J

American journal of epidemiology

2006 Volume 164, Issue 8, Page(s) 794–804

Abstract: Single nucleotide polymorphisms (SNPs) are the most common form of human genetic variation, with millions present in the human genome. Because only 1% might be expected to confer more than modest individual effects in association studies, the selection ... ...

Abstract	Single nucleotide polymorphisms (SNPs) are the most common form of human genetic variation, with millions present in the human genome. Because only 1% might be expected to confer more than modest individual effects in association studies, the selection of predictive candidate variants for complex disease analyses is formidable. Technologic advances in SNP discovery and the ever-changing annotation of the genome have led to massive informational resources that can be difficult to master across disciplines. A simplified guide is needed. Although methods for evaluating nonsynonymous coding SNPs are known, several other publicly available computational tools can be utilized to assess polymorphic variants in noncoding regions. As an example, the authors applied multiple methods to select SNPs in DNA double-strand break repair genes. They chose to evaluate SNPs that occurred among a preexisting set of 57 validated assays and to justify new assay development for 83 potential SNPs in the DNA-dependent protein kinase catalytic subunit. Of the 140 SNPs, the authors eliminated 119 variants with low or neutral predictions. The existing computational methods they used and the semiquantitative relative ranking strategy they developed can be adapted to a priori SNP selection or post hoc evaluation of variants identified in whole genome scans or within haplotype blocks associated with disease. The authors show a "real world" application of some existing bioinformatics tools for use in large epidemiologic studies and genetic analyses. They also reviewed alternative approaches that provide related information.
MeSH term(s)	Algorithms ; Amino Acid Sequence ; Base Sequence ; Epidemiologic Methods ; Genetic Predisposition to Disease ; Humans ; Internet ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2006-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2937-3
ISSN	1476-6256 ; 0002-9262
ISSN (online)	1476-6256
ISSN	0002-9262
DOI	10.1093/aje/kwj269
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Article ; Online: Meeting research needs with postmortem biospecimen donation: summary of recommendations for postmortem recovery of normal human biospecimens for research.

Mucci, Neil R / Moore, Helen M / Brigham, Lori E / Goldthwaite, Charles A / Little, A Roger / Lockhart, Nicole C / Scott, Michael P / Struewing, Jeffery P / Vincent, Stephen L / Compton, Carolyn C

Biopreservation and biobanking

2013 Volume 11, Issue 2, Page(s) 77–82

Abstract: Normal human tissues, bodily fluids, and other biospecimens of known quality are essential for research to understand the development of cancer and other diseases and to develop new diagnostics and therapies. However, obtaining normal biospecimens ... ...

Abstract	Normal human tissues, bodily fluids, and other biospecimens of known quality are essential for research to understand the development of cancer and other diseases and to develop new diagnostics and therapies. However, obtaining normal biospecimens appropriate for contemporary large-scale molecular and genomic research is one of the most challenging biospecimen acquisition problems for scientists and biospecimen resources that support research. Recognizing this challenge, the U.S. National Cancer Institute recently convened a series of workshops and meetings focused on the acquisition of normal tissues for research and produced an extensive document, Recommendations for Postmortem Recovery of Normal Human Biospecimens for Research. This article summarizes these recommendations, addressing key ethical, operational, and scientific elements for collecting normal reference biospecimens from postmortem donors in the U.S. Awareness of these recommendations can foster more effective collaborations and mitigate potential logistical challenges, while promoting postmortem biospecimen donation options for families and increasing the availability of high quality normal biospecimens for research. The recommendations have been put into practice in the collection of normal human biospecimens for the NIH Genotype-Tissue Expression Program (GTEx), a pilot study of human gene expression and regulation in multiple tissues which will provide valuable insights into the mechanisms of gene regulation and, in the future, its disease-related perturbations (http://commonfund.nih.gov/GTEx/).
MeSH term(s)	Autopsy ; Biomedical Research ; Family ; Guidelines as Topic ; Humans ; Postmortem Changes ; Quality Control ; Residence Characteristics ; Social Control, Formal ; Tissue Banks/ethics ; Tissue Banks/legislation & jurisprudence ; Tissue Donors
Language	English
Publishing date	2013-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2593993-2
ISSN	1947-5543 ; 1947-5535
ISSN (online)	1947-5543
ISSN	1947-5535
DOI	10.1089/bio.2012.0063
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