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Article ; Online: BRCA1/2

Shah, Payal D / Nathanson, Katherine L

2024 Volume 109, Issue 1, Page(s) 21–22

MeSH term(s)	Humans ; BRCA1 Protein/genetics ; BRCA2 Protein/genetics ; Mutation ; Hematologic Neoplasms/diagnosis ; Hematologic Neoplasms/genetics
Chemical Substances	BRCA1 protein, human ; BRCA1 Protein ; BRCA2 protein, human ; BRCA2 Protein
Language	English
Publishing date	2024-01-01
Publishing country	Italy
Document type	Journal Article
ZDB-ID	2333-4
ISSN	1592-8721 ; 0017-6567 ; 0390-6078
ISSN (online)	1592-8721
ISSN	0017-6567 ; 0390-6078
DOI	10.3324/haematol.2023.283348
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Article: Real-world evaluation of deep learning algorithms to classify functional pathogenic germline variants.

Chow, Ryan D / Parikh, Ravi B / Nathanson, Katherine L

medRxiv : the preprint server for health sciences

2024

Abstract: Deep learning models for variant pathogenicity prediction can recapitulate expert-curated annotations, but their performance remains unexplored on actual disease phenotypes in a real-world setting. Here, we apply three state-of-the-art pathogenicity ... ...

Abstract	Deep learning models for variant pathogenicity prediction can recapitulate expert-curated annotations, but their performance remains unexplored on actual disease phenotypes in a real-world setting. Here, we apply three state-of-the-art pathogenicity prediction models to classify hereditary breast cancer gene variants in the UK Biobank. Predicted pathogenic variants in
Language	English
Publishing date	2024-04-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.05.24305402
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Article ; Online: Nationwide Trends and Determinants of Germline BRCA1/2 Testing in Patients With Breast and Ovarian Cancer.

Lau-Min, Kelsey S / McCarthy, Anne Marie / Nathanson, Katherine L / Domchek, Susan M

Journal of the National Comprehensive Cancer Network : JNCCN

2023 Volume 21, Issue 4, Page(s) 351–358.e4

Abstract: Background: Germline genetic testing (GT) for BRCA1/2 is instrumental in identifying patients with breast and ovarian cancers who are eligible for PARP inhibitors (PARPi). Little is known about recent trends and determinants of GT since PARPi were ... ...

Abstract	Background: Germline genetic testing (GT) for BRCA1/2 is instrumental in identifying patients with breast and ovarian cancers who are eligible for PARP inhibitors (PARPi). Little is known about recent trends and determinants of GT since PARPi were approved for these patients. Patients and methods: We performed a retrospective cohort study of patients in a nationwide electronic health record (EHR)-derived oncology-specific database with the following GT eligibility criteria: breast cancer diagnosed at age ≤45 years, triple-negative breast cancer diagnosed at age ≤60 years, male breast cancer, or ovarian cancer. GT within 1 year of diagnosis was assessed and stratified by tumor type. Multivariable log-binomial regressions estimated adjusted relative risks (RRs) of GT by patient and tumor characteristics. Results: Among 2,982 eligible patients with breast cancer, 56.4% underwent GT between January 2011 and March 2020, with a significant increase in GT over time (RR, 1.08; 95% CI, 1.05-1.11, for each year), independent of when PARPi were approved for BRCA1/2-mutated metastatic breast cancer in January 2018. In multivariable analyses, older age (RR, 0.93; 95% CI, 0.90-0.96, for every 5 years) and Medicare coverage (RR, 0.69; 95% CI, 0.49-0.96 vs commercial insurance) were associated with less GT. Among 5,563 eligible patients with ovarian cancer, 35.4% underwent GT between January 2011 and March 2020, with a significant increase in GT over time (RR, 1.11; 95% CI, 1.07-1.14, for each year) that accelerated after approval of PARPi for BRCA1/2-mutated, chemotherapy-refractory ovarian cancer in December 2014 (RR, 1.42; 95% CI, 1.19-1.70). Older age (RR, 0.95; 95% CI, 0.93-0.97, for every 5 years) and Black or African American race (RR, 0.80; 95% CI, 0.65-0.98 vs White race) were associated with less GT. Conclusions: GT remains underutilized nationwide among patients with breast and ovarian cancers. Although GT has increased over time, significant disparities by age, race, and insurance status persist. Additional work is needed to design, implement, and evaluate strategies to ensure that all eligible patients receive GT.
MeSH term(s)	United States/epidemiology ; Humans ; Male ; Aged ; Female ; Middle Aged ; Retrospective Studies ; Medicare ; BRCA1 Protein/genetics ; Ovarian Neoplasms/diagnosis ; Ovarian Neoplasms/epidemiology ; Ovarian Neoplasms/genetics ; Breast Neoplasms/diagnosis ; Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Genetic Testing ; Triple Negative Breast Neoplasms/pathology ; Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use
Chemical Substances	BRCA1 Protein ; Poly(ADP-ribose) Polymerase Inhibitors ; BRCA1 protein, human
Language	English
Publishing date	2023-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2250759-0
ISSN	1540-1413 ; 1540-1405
ISSN (online)	1540-1413
ISSN	1540-1405
DOI	10.6004/jnccn.2022.7257
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Article ; Online: Retrospective Survival Analysis of Patients With Advanced Pancreatic Ductal Adenocarcinoma and Germline

Reiss, Kim A / Yu, Shun / Judy, Renae / Symecko, Heather / Nathanson, Katherine L / Domchek, Susan M

JCO precision oncology

2022 Volume 2, Page(s) 1–9

Abstract: Purpose: Germline mutations in the homologous recombination (HR) genes : Materials and methods: Twenty-nine individuals with deleterious germline mutations in : Results: Patients who were mut-positive had an OS of 21.8 months; control patients had ...

Abstract	Purpose: Germline mutations in the homologous recombination (HR) genes Materials and methods: Twenty-nine individuals with deleterious germline mutations in Results: Patients who were mut-positive had an OS of 21.8 months; control patients had an OS of 8.1 months (hazard ratio [HR], 0.35; 95% CI, 0.2 to 0.62; Conclusion: Platinum-based therapy may confer a survival benefit in patients with advanced PDAC who carry a deleterious germline
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.17.00152
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Article ; Online: Uncommon variants in FLG2 and TCHHL1 are associated with remission of atopic dermatitis in a large longitudinal US cohort.

Berna, Ronald / Mitra, Nandita / Hoffstad, Ole / Wubbenhorst, Bradley / Nathanson, Katherine L / Margolis, David J

Archives of dermatological research

2022 Volume 314, Issue 10, Page(s) 953–959

Abstract: Atopic dermatitis (AD) is a relapsing inflammatory skin disease; filaggrin (FLG) variation has been consistently associated with its pathogenesis. Filaggrin-2 (FLG2) and trichohyalin-like-1 (TCHHL1) are members of the same protein family (S100 fused-type ...

Abstract	Atopic dermatitis (AD) is a relapsing inflammatory skin disease; filaggrin (FLG) variation has been consistently associated with its pathogenesis. Filaggrin-2 (FLG2) and trichohyalin-like-1 (TCHHL1) are members of the same protein family (S100 fused-type proteins), are similar in structure to FLG, and may be involved in AD pathogenesis. We sought to evaluate the association between variation in FLG2, TCHHL1 and AD remission. We sequenced FLG2 and TCHHL1 in a longitudinal AD cohort using targeted capture-based massively parallel sequencing. Association between individual alleles and AD remission was evaluated with generalized estimating equations for binary outcomes. Association between groups of alleles and AD remission was evaluated using a genetic algorithm to group alleles. We identified two loss-of-function (LoF) mutations in FLG2 (Ser2377Ter, Arg2207Ter) and 2 LoF mutations in TCHHL1 (Gln656Ter, Gln294Ter), none of which were associated with AD remission. Common (MAF > 5%) alleles in FLG2 were similarly unassociated with AD. No common alleles in TCHHL1 were associated with AD remission after multiple testing correction. Among self-described whites, a group of 34 uncommon alleles in FLG2 were associated with increased AD remission (OR 7.64e17; 95% CI 4.41e17-1.32e18; adjusted p < 1.0e-16). Twelve uncommon alleles in TCHHL1 trended toward association with increased AD remission (OR 23.46; 95% CI 7.07-77.89; adjusted p = 0.064). Among self-described African Americans, 13 uncommon FLG2 alleles were associated with increased AD remission (OR 21.01; 95% CI 11.90-37.09; adjusted p < 1.0e-16). No TCHHL1 uncommon allele groups were associated with AD remission among African Americans. Our study supports the role of uncommon alleles in FLG2 and TCHHL1 in AD pathogenesis.
MeSH term(s)	Alleles ; Cohort Studies ; Dermatitis, Atopic/pathology ; Filaggrin Proteins ; Humans ; Intermediate Filament Proteins/genetics ; Intermediate Filament Proteins/metabolism ; Mutation ; S100 Proteins ; White People
Chemical Substances	FLG2 protein, human ; Filaggrin Proteins ; Intermediate Filament Proteins ; S100 Proteins ; TCHHL1 protein, human
Language	English
Publishing date	2022-01-04
Publishing country	Germany
Document type	Journal Article
ZDB-ID	130131-7
ISSN	1432-069X ; 0340-3696
ISSN (online)	1432-069X
ISSN	0340-3696
DOI	10.1007/s00403-021-02319-7
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Article ; Online: Pheochromocytoma and Paraganglioma Susceptibility Genes: Estimating the Associated Risk of Disease.

Fishbein, Lauren / Nathanson, Katherine L

JAMA oncology

2017 Volume 3, Issue 9, Page(s) 1212–1213

MeSH term(s)	Adrenal Gland Neoplasms/genetics ; Electron Transport Complex II ; Humans ; Membrane Proteins/genetics ; Paraganglioma/genetics ; Pheochromocytoma/genetics
Chemical Substances	Membrane Proteins ; TMEM127 protein, human ; Electron Transport Complex II (EC 1.3.5.1) ; SDHA protein, human (EC 1.3.5.1)
Language	English
Publishing date	2017-05-30
Publishing country	United States
Document type	Journal Article ; Comment
ISSN	2374-2445
ISSN (online)	2374-2445
DOI	10.1001/jamaoncol.2017.0222
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Article: Homologous recombination pathway gene variants identified by tumor-only sequencing assays in lung carcinoma patients.

Yoon, Ju-Yoon / Roth, Jacquelyn J / Rushton, Chase A / Morrissette, Jennifer J D / Nathanson, Katherine L / Cohen, Roger B / Rosenbaum, Jason N

Translational lung cancer research

2023 Volume 12, Issue 6, Page(s) 1236–1244

Abstract: Background: The homologous recombination (HR) repair pathway plays a key role in double-stranded DNA break repair, and germline HR pathway gene variants are associated with increased risk of several cancers, including breast and ovarian cancer. HR ... ...

Abstract	Background: The homologous recombination (HR) repair pathway plays a key role in double-stranded DNA break repair, and germline HR pathway gene variants are associated with increased risk of several cancers, including breast and ovarian cancer. HR deficiency is also a therapeutically targetable phenotype. Methods: Somatic (tumour-only) sequencing was performed on 1,109 cases of lung tumors, and the pathological data were reviewed to filter for lung primary carcinomas. Cases were filtered for variants (disease-associated or of uncertain significance) in 14 HR pathway genes, including Results: Sixty-one HR pathway gene variants in 56 patients with primary lung cancer were identified. Further filtering by variant allele fraction (VAF) of ≥30% identified 17 HR pathway gene variants in 17 patients. Conclusions: Genomic variants in the HR repair pathway identified in tumor-only sequencing and occurring at higher VAFs (i.e., ≥30%) may suggest a germline origin. Correlating with personal and family history, a subset of these variants is also suggested to be associated with familial cancer risks. Patient age, smoking history and driver mutation status are expected to be a poor screening tool in identifying these patients. Finally, the relative enrichment for
Language	English
Publishing date	2023-06-08
Publishing country	China
Document type	Journal Article
ZDB-ID	2754335-3
ISSN	2226-4477 ; 2218-6751
ISSN (online)	2226-4477
ISSN	2218-6751
DOI	10.21037/tlcr-22-749
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Article ; Online: Application of Panel-Based Tests for Inherited Risk of Cancer.

Shah, Payal D / Nathanson, Katherine L

Annual review of genomics and human genetics

2017 Volume 18, Page(s) 201–227

Abstract: Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in ... ...

Abstract	Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in clinical settings, understanding their clinical validity and utility is critical. When evaluating the inherited risk of breast and ovarian cancers, panel-based tests provide incremental benefit compared with BRCA1/2 genetic testing. For inherited risk of other cancers, such as colon cancer and pheochromocytoma-paraganglioma, the clinical utility and yield of panel-based testing are higher; in fact, simultaneous evaluation of multiple genes has been the historical standard for these diseases. Evaluating inherited risk with panel-based testing has recently entered clinical practice for prostate and pancreatic cancers, with potential therapeutic implications. The resulting variants of uncertain significance and mutations with unclear actionability pose challenges to service providers and patients, underscoring the importance of genetic counseling and data-sharing initiatives. This review explores the evolving merits, challenges, and nuances of panel-based testing for cancer susceptibility.
MeSH term(s)	Female ; Genetic Predisposition to Disease ; Genetic Testing/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Mutation ; Neoplasms/genetics
Language	English
Publishing date	2017-05-15
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2037670-4
ISSN	1545-293X ; 1527-8204
ISSN (online)	1545-293X
ISSN	1527-8204
DOI	10.1146/annurev-genom-091416-035305
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Article ; Online: A practical guide for evaluating gonadal germ cell tumor predisposition in differences of sex development.

Pyle, Louise C / Nathanson, Katherine L

American journal of medical genetics. Part C, Seminars in medical genetics

2017 Volume 175, Issue 2, Page(s) 304–314

Abstract: Differences of Sex Development (DSD) includes a wide spectrum of etiologies and phenotypes. A subset of individuals with DSDs are predisposed to gonadal germ cell tumor (GCT). In this setting, GCT risk varies widely, depending on the DSD molecular ... ...

Abstract	Differences of Sex Development (DSD) includes a wide spectrum of etiologies and phenotypes. A subset of individuals with DSDs are predisposed to gonadal germ cell tumor (GCT). In this setting, GCT risk varies widely, depending on the DSD molecular etiology and penetrance. Prognostication based on molecular diagnosis remains challenging, as natural history data specific to recently identified molecular causes of DSD is lacking. In this review, we provide a framework for the clinical geneticist to consider GCT tumor risk in the patient with DSD. We discuss germ cell development and etiology of GCT growth, along with parameters to consider when recommending prophylactic gonadectomy including fertility, hormonal output, and malignant GTC treatment outcomes. Shortly after the 2006 reorganization of DSD nomenclature, literature reviews of natural history publications stratified GCT risk by a chromosomal, pathological, and hormonal taxonomy. Our 2017 literature review reveals a larger body of publications. However, the broad DSD GCT risk stratification within the 2006 taxonomy remains stable. We discuss precise GCT risk assessment for specific diagnoses, including androgen insensitivity, Smith-Lemli-Opitz, and 46,XY with MAP3K1 mutations and gonadal dysgenesis, as examples. We also examine the GCT risk in non-DSD syndromes, in addition to the cancer risks in DSD patients with dimorphic gonads and genitalia. This review is intended to provide a nuanced assessment of relative germ cell tumor risk in the DSD patient, including modern precise molecular diagnosis, for use by the clinical geneticist.
Language	English
Publishing date	2017-06
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2108622-9
ISSN	1552-4876 ; 0148-7299 ; 1552-4868
ISSN (online)	1552-4876
ISSN	0148-7299 ; 1552-4868
DOI	10.1002/ajmg.c.31562
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Article: Clinical management of TP53 mosaic variants found on germline genetic testing.

Ward, Abigail / Farengo-Clark, Dana / McKenna, Danielle B / Safonov, Anton / Good, Madeline / Le, Anh / Kessler, Lisa / Shah, Payal D / Bradbury, Angela R / Domchek, Susan M / Nathanson, Katherine L / Powers, Jacquelyn / Maxwell, Kara N

Cancer genetics

2024 Volume 284-285, Page(s) 43–47

Abstract: Background: Germline heterozygous TP53 pathogenic variants (PVs) cause Li Fraumeni Syndrome (LFS, OMIM#151623). TP53 PVs at lower-than-expected variant allele frequencies (VAF) may reflect postzygotic mosaicism (PZM) or clonal hematopoiesis (CH); ... ...

Abstract	Background: Germline heterozygous TP53 pathogenic variants (PVs) cause Li Fraumeni Syndrome (LFS, OMIM#151623). TP53 PVs at lower-than-expected variant allele frequencies (VAF) may reflect postzygotic mosaicism (PZM) or clonal hematopoiesis (CH); however, no guidelines exist for workup and clinical management. Patients and methods: Retrospective analysis of probands who presented to an academic cancer genetics program with a TP53 PV result on germline genetic testing. Results: Twenty-one of 125 unrelated probands (17 %) were found to harbor a TP53 PV with VAF<30 % or a designation of "mosaic". A diagnosis of PZM was made in nine (43 %) due to a clinical phenotype consistent with LFS with (n = 8) or without (n = 1) positive ancillary tissue testing. Twelve patients (57 %) were diagnosed with presumed CH (pCH) due to a diagnosis of a myeloproliferative neoplasm, negative ancillary tissue testing, clinical phenotype not meeting LFS criteria, no cancer, and/or no first cancer age<50. Of the 19 patients with biological offspring, nine had either partial or complete offspring testing, all negative. Conclusions: Determining the etiology of low VAF TP53 PVs requires ancillary tissue testing and incorporation of clinical phenotype. Discerning PZM versus CH is important to provide optimal care and follow-up.
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2599227-2
ISSN	2210-7762
ISSN	2210-7762
DOI	10.1016/j.cancergen.2024.04.002
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