Supp Figure 2: Comparison of the MSK-IMPACT Cervical Cancer Cohort and the TCGA cohort for patients with Stages I-IVA disease. HPV, human papillomavirus; IMPACT, Memorial Sloan Kettering Cancer Center – Integrated Mutation Profiling of Actionable Cancer Targets; TCGA, The Cancer Genome Atlas

10.1158/1078-0432.24558681.v1

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Supplementary Figure S1 from Assessing the Genomic Landscape of Cervical Cancers: Clinical Opportunities and Therapeutic Targets

Claire F. Friedman Vignesh Ravichandran Kathryn Miller Chad Vanderbilt Qin Zhou

Supp Figure 1: OncoKB Theapeutic Levels of Evidence

10.1158/1078-0432.24558684.v1

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TERT promoter mutations and gene amplification in endometrial cancer

Gynecologic Oncology (2023)

Aaron Praiss Antonio Marra Qin Zhou Eric Rios‐Doria Amir Momeni Boroujeni

10.1016/j.ygyno.2023.10.007

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Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes

Nature Communications (2017)

Nadeem Riaz Pedro Blecua Raymond S. Lim Ronglai Shen Daniel S. Higginson

BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in a syndrome of hereditary breast and ovarian cancer (HBOC). Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact on other cancers remains to be fully elucidated. Here, we perform a pan-cancer analysis of The Cancer Genome Atlas (TCGA) data set and observe that bi-allelic pathogenic alterations in homologous recombination (HR) DNA repair-related genes are prevalent across many malignancies. These bi-allelic alterations often associate with genomic features of HR deficiency. Further, in ovarian, breast and prostate cancers, bi-allelic alterations are mutually exclusive of each other. The combination of these two properties facilitates reclassification of variants of unknown significance affecting DNA repair genes, and may help personalize HR directed therapies in the clinic.Germline mutations in homologous recombination (HR) DNA repair genes are linked to breast and ovarian cancer. Here, the authors show that mutually exclusive bi-allelic inactivation of HR genes are present in other cancer types and associated with genomic features of HR deficiency, expanding the potential use of HR-directed therapies.

BRCA2 Protein

Non-allelic homologous recombination

10.1038/s41467-017-00921-w

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Supplementary Figure S1 from The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas

Charlotte K.Y. Ng Salvatore Piscuoglio Felipe C. Geyer Kathleen A. Burke Fresia Pareja

Supplementary Fig. S1. Estrogen receptor (ER) and progesterone receptor (PR) status of MTC18 and HER2 status of MTC23 and representative Sanger sequencing traces for validated mutations. (a) Representative micrograph of a hematoxylin and eosin-stained slide of case MTC18 with (b) 1% of cells weakly expressing ER and (c) 20% of cells weakly expressing PR. (d) Representative micrograph of case MTC23 (e) lacking HER2 expression by immunohistochemistry but (f) harboring HER2 gene amplification by fluorescence in situ hybridization. (g) Genome plot of MTC23 showing HER2 gene amplification. In the genome plot, smoothed Log2 ratios (y-axis) were plotted according to their genomic positions (x-axis). The red arrow points at the HER2 gene locus. (h) Representative Sanger sequencing traces for validated mutations. Original magnification of micrographs and immunohistochemical staining 200x. Scale bar: 500 μm.

Sanger sequencing

10.1158/1078-0432.22466760.v1

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Supplementary Table S4 from The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas

Charlotte K.Y. Ng Salvatore Piscuoglio Felipe C. Geyer Kathleen A. Burke Fresia Pareja

Supplementary Table S4: Significantly mutated genes analysis of metaplastic breast cancers (n=35) using MutSigCV and the algorithm proposed by Youn and Simon.

Metaplastic Carcinoma

Table (database)

10.1158/1078-0432.22466733.v1

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Supplementary Table S6 from The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas

Charlotte K.Y. Ng Salvatore Piscuoglio Felipe C. Geyer Kathleen A. Burke Fresia Pareja

Supplementary Table S6: Comparative analysis of the mutational frequencies of genes affecting selected functional pathways in metaplastic breast cancers and triple-negative invasive ductal carcinomas of no special type and correlations of mutational status with clinicopathologic parameters. p<0.05 are highlighted in bold. *: Fisher's exact test. **: Mann-Whitney U-test.

10.1158/1078-0432.22466727.v1

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