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Recognized by America's Top Doctors 2015 – 2017
Recognized in Philadelphia magazine's annual Top Docs issues from 2018 - 2021
Perelman Center for Advanced Medicine
South Pavilion, 1st Floor
3400 Civic Center Boulevard
Philadelphia, PA 19104
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Hereditary Breast CancerThe research in the Nathanson Group in hereditary breast and ovarian cancer started when I was post-doctoral fellow, training under Dr. Barbara Weber. Most recently, we have published studies demonstrating variable risks of breast and ovarian cancers with differing mutation types and locations with BRCA1 and BRCA2 (JAMA, 2015), and described the world-wide distribution of mutations (Hum Mutat, 2018). My group has evaluated the rate of moderate risk gene mutations in early onset breast cancer (Genet Med, 2015; NPJ Breast Cancer ,2017), contributed to consensus statements on the risk of these mutations (NEJM, 2015; Nat Rev Clinic Oncol, 2016), and evaluated the use of the ACMG guidelines for variant annotation of these genes (Am J Hum Genet, 2016). We published a somatic characterization of tumors associated with BRCA1/2 germline mutations and demonstrated that a significant proportion do not have allele-specific loss of heterozygosity, associated with differential genetic/genomic characteristics and survival after treatment (Nat Comm, 2017). We have preliminary data following up.Example Projects:1) Identification of novel breast cancer susceptibility genes using large scale sequencing in high risk and case-control cohort studies2) Characterization of moderate penetrance breast cancer susceptibility genes in large cohorts3) Characterization of immunogenicity in BRCA1/2 mutation associated cancers, understanding the associated molecular features and role of aneuploidy (working with cancer immunologists at Penn Medicine)4) Understanding tumor heterogeneity in BRCA1/2 mutation associated cancers, by using single cell sequencing, high-depth targeted sequencing and large scale5) Working with Dr. E. John Wherry’s group to elucidate immune function in healthy BRCA1/2 mutation carriersMelanomaOur research efforts in melanoma have spanned the past decade. Over this time period, we have worked with Dr. Meenhard Herlyn’s group at the Wistar Institute to lead efforts on the genetic and genomic characterization of cell lines and PDX used in pre-clinical modeling in melanoma, working, leading to over 25 publications focusing on intrinsic and acquired resistance to multiple different types of therapies. This effort cumulated in the publication of targeted massively parallel sequencing to characterize over 450 tumors, cell lines and patient derived xenografts (PDX) (Cell Reports, 2017). In the past, we also have worked on correlative studies in conjunction with clinical trials. We have two funded projects investigating inherited variation in association with outcome and immune related adverse events after treatment with checkpoint blockade, which are coming to fruition. Building upon our experience in massively parallel sequencing, the project we are doing on inherited variation in association with response to ipilimumab and our location within the Institute for Immunology, in the past two years, we also have worked on interdisciplinary projects that involve both cancer genetics and cancer immunology, specifically in melanoma (Nature, 2017; Nature Medicine, 2019), and have a funded core for massively parallel sequencing and analysis for the P01 Radiation – Immuno-oncology P01.Example Projects:1) Evaluating the intersection and function of non-canonical BRAF mutations with other MAPK mutations using single cell sequencing2) Compilation of data on over 600 melanoma cell lines, PDX and tumor biopsies for in-depth analysis, with a particular view to determining if homologous recombination deficiency scores can be calculated from the targeted sequencing data (and correlate with mutation status)3) Analysis of data on association of response and immune related adverse events after treatment with ipilimumab, focusing on specific pathways and HLA groups4) Analysis of data on association of response and immune related adverse events after treatment with nivolumab and combination therapy (nivolumab and ipilimumab), focusing on specific pathways and HLA groupsTesticular Germ Cell TumorWe identified the first (and only) validated candidate region associated with increased risk of TGCT in 2005 and went on to co-publish one of initial genome wide association studies (GWAS) study in TGCT (Nat Genet, 2009). GWAS in TGCT are the most successful in cancer, in terms of identifying loci with high effect sizes containing biologically plausible genes, which have implicated differences in male germ cell maturation and differentiation as being critical to disease susceptibility. We have subsequently published several other studies identifying loci associated with risk of TGCT. I currently lead the Testicular Cancer Association Consortium (TECAC), which is an international consortium of researchers (Nat Genet, 2009; Hum Mol Genet, 2011; Nat Genet, 2013; Hum Mol Genet, 2013; Hum Mol Genet, 2014; Nat Genet, 2017). These studies have furthered our understanding of the biology of TGCT as being a disease of male germ cell development, led to important genetic insights into the epidemiology of TGCT and identified the most significant loci (highest odds ratios) of any cancer GWAS. We also have generated whole exome data on several 100 patients with TGCT (JAMA Oncol, 2019), and plan more extensive sequencing, and have done ATAC-seq and Spatial-Seq (chromatin conformation capture) on multiple TGCT cell lines for post-GWA functional studies. We also heavily participated in the TCGA TGCT effort and have an ongoing collaborative project with multiple participants supported by Movember to evaluate resistance to Cisplatin in patients with TGCT.Example Projects:1) Identification of causal variants (SNPs) in regions associated with TGCT through in silico analysis, and subsequent functional/experimental evaluation2) HiChIP (chromosome conformation capture using few input cells) in fetal and adult germ cells to define target-enhancer connectome and identify causal variants for TGCT3) Whole genome sequencing of high-risk individuals with TGCT (bilateral, family history, non-white)4) Follow-up from whole exome sequencing in case-control study to validate rare variants/genes in association with TGCT5) Initiation and development of studies in non-whites with TGCT and women with ovarian germ tumors (also using social media)Neuroendocrine TumorsThe Nathanson group works collaboratively with the Neuroendocrine Tumor Center at Penn Medicine on the genetics of pheochromocytoma and paraganglioma (PCC/PGL). They published their clinical genetic testing experience in PCC/PGL (Ann Surg Oncol, 2013), showing an inherited mutation rate of over 40%, accompanied by an editorial encouraging other clinicians to follow their paradigm for clinical genetic testing her group has established at Penn. Her group also was the first to identify somatic mutations in ATRX, associated with clinically aggressive disease (Nat Comm, 2015). Further, she co-led the Cancer Genome Atlas effort in PCC/PGL, which had multiple novel findings, including a recurrent fusion protein specific to this disease, and genetic/genomic predictors of poor prognosis (Cancer Cell, 2017). The group is continuing to collect samples from patients with PCC/PGL and SDHx mutations for further study.Example Projects:1) Evaluation of matched tumors – primary and recurrent PCC/PGL to identify mutations associated with metastatic disease2) Evaluation of whole genome sequencing of PCC/PGL patients with no identified inherited mutations3) Follow-up on studies suggesting that PCC/PGL with SDHx mutations have a BRCA-like phenotype, evaluating homologous recombination deficiency scores and PARP tracer up-take
Boddicker NJ, Hu C, Weitzel JN, Kraft P, Nathanson KL, Goldgar DE, Na J, Huang H, Gnanaolivu RD, Larson N, Yussuf A, Yao S, Vachon CM, Trentham-Dietz A, Teras L, Taylor JA, Scott CE, Sandler DP, Pesaran T, Patel AV, Palmer JR, Ong IM, Olson JE, O'Brien K, Neuhausen S, Martinez E, Ma H, Lindstrom S, Le Marchand L, Kooperberg C, Karam R, Hunter DJ, Hodge JM, Haiman C, Gaudet MM, Gao C, LaDuca H, Lacey JV, Dolinsky JS, Chao E, Carter BD, Burnside ES, Bertrand KA, Bernstein L, Auer PW, Ambrosone C, Yadav S, Hart SN, Polley EC, Domchek SM, Couch FJ.: Risk of Late-Onset Breast Cancer in Genetically Predisposed Women J Clin Oncol. 39 (31): 3430-3440,2021.
Yadav S, Hu C, Nathanson KL, Weitzel JN, Goldgar DE, Kraft P, Gnanaolivu RD, Na J, Huang H, Boddicker NJ, Larson N, Gao C, Yao S, Weinberg C, Vachon CM, Trentham-Dietz A, Taylor JA, Sandler DR, Patel A, Palmer JR, Olson JE, Neuhausen S, Martinez E, Lindstrom S, Lacey JV, Kurian AW, John EM, Haiman C, Bernstein L, Auer PW, Anton-Culver H, Ambrosone CB, Karam R, Chao E, Yussuf A, Pesaran T, Dolinsky JS, Hart SN, LaDuca H, Polley EC, Domchek SM, Couch FJ: Germline Pathogenic Variants in Cancer Predisposition Genes Among Women With Invasive Lobular Carcinoma of the Breast J Clin Oncol : 2021.
Lakeman IMM, van den Broek AJ, Vos JAM, Barnes DR, Adlard J, Andrulis IL, Arason A, Arnold N, Arun BK, Balmaña J, Barrowdale D, Benitez J, Borg A, Caldés T, Caligo MA, Chung WK, Claes KBM; GEMO Study Collaborators; EMBRACE Collaborators, Collée JM, Couch FJ, Daly MB, Dennis J, Dhawan M, Domchek SM, Eeles R, Engel C, Evans DG, Feliubadaló L, Foretova L, Friedman E, Frost D, Ganz PA, Garber J, Gayther SA, Gerdes AM, Godwin AK, Goldgar DE, Hahnen E, Hake CR, Hamann U, Hogervorst FBL, Hooning MJ, Hopper JL, Hulick PJ, Imyanitov EN; OCGN Investigators; HEBON Investigators; KconFab Investigators, Isaacs C, Izatt L, Jakubowska A, James PA, Janavicius R, Jensen UB, Jiao Y, John EM, Joseph V, Karlan BY, Kets CM, Konstantopoulou I, Kwong A, Legrand C, Leslie G, Lesueur F, Loud JT, Lubiński J, Manoukian S, McGuffog L, Miller A, Gomes DM, Montagna M, Mouret-Fourme E, Nathanson KL, Neuhausen SL, Nevanlinna H, Yie JNY, Olah E, Olopade OI, Park SK, Parsons MT, Peterlongo P, Piedmonte M, Radice P, Rantala J, Rennert G, Risch HA, Schmutzler RK, Sharma P, Simard J, Singer CF, Stadler Z, Stoppa-Lyonnet D, Sutter C, Tan YY, Teixeira MR, Teo SH, Teulé A, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Tung N, van Rensburg EJ, Vega A, Wappenschmidt B, Devilee P, van Asperen CJ, Bernstein JL, Offit K, Easton DF, Rookus MA, Chenevix-Trench G, Antoniou AC, Robson M, Schmidt MK.: The predictive ability of the 313 variant-based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant Genet Med 23 (9): 1726-1737,2021.
Alzofon N, Koc K, Panwell K, Pozdeyev N, Marshall CB, Albuja-Cruz M, Raeburn CD, Nathanson KL, Cohen DL, Wierman ME, Kiseljak-Vassiliades K, Fishbein L: Mastermind Like Transcriptional Coactivator 3 (MAML3) Drives Neuroendocrine Tumor Progression Mol Cancer Res
19 (9): 1476-1485,2021.
Du Z, Gao G, Adedokun B, Ahearn T, Lunetta KL, Zirpoli G, Troester MA, Ruiz-Narváez EA, Haddad SA, Pal Choudhury P, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Mancuso N, Press MF, Deming SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbe O, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Sandler DP, Taylor JA, Wang Q, Weinberg CR, Kitahara CM, Blot W, Nathanson KL, Hennis A, Nemesure B, Ambs S, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Olshan AF, Ambrosone CB, Olopade OI, Yarney J, Awuah B, Addai Wiafe B, Conti DV; GBHS Study Team, Palmer JR, Garcia-Closas M, Huo D, Haiman CA.: Evaluating Polygenic Risk Scores for Breast Cancer in Women of African Ancestry J Natl Cancer Inst 113 (9): 1168-1176,2021.
Xu H, George E, Kinose Y, Kim H, Shah JB, Peake JD, Ferman B, Medvedev S, Murtha T, Barger CJ, Devins KM, D'Andrea K, Wubbenhorst B, Schwartz LE, Hwang WT, Mills GB, Nathanson KL, Karpf AR, Drapkin R, Brown EJ, Simpkins F: CCNE1 copy number is a biomarker for response to combination WEE1-ATR inhibition in ovarian and endometrial cancer models Cell Rep Med 2 (9): eCollection,2021.
Bratslavsky G, Mendhiratta N, Daneshvar M, Brugarolas J, Ball MW, Metwalli A, Nathanson KL, Pierorazio PM, Boris RS, Singer EA, Carlo MI, Daly MB, Henske EP, Hyatt C, Middleton L, Morris G, Jeong A, Narayan V, Rathmell WK, Vaishampayan U, Lee BH, Battle D, Hall MJ, Hafez K, Jewett MAS, Karamboulas C, Pal SK, Hakimi AA, Kutikov A, Iliopoulos O, Linehan WM, Jonasch E, Srinivasan R, Shuch B: Genetic risk assessment for hereditary renal cell carcinoma: Clinical consensus statement. Cancer 127 (21): Epub,2021.
Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, Dipersio JF; NCI PDXNet Consortium, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment Nat Commun 12 (1): 2021.
Gao C, Polley EC, Hart SN, Huang H, Hu C, Gnanaolivu R, Lilyquist J, Boddicker NJ, Na J, Ambrosone CB, Auer PL, Bernstein L, Burnside ES, Eliassen AH, Gaudet MM, Haiman C, Hunter DJ, Jacobs EJ, John EM, Lindström S, Ma H, Neuhausen SL, Newcomb PA, O'Brien KM, Olson JE, Ong IM, Patel AV, Palmer JR, Sandler DP, Tamimi R, Taylor JA, Teras LR, Trentham-Dietz A, Vachon CM, Weinberg CR, Yao S, Weitzel JN, Goldgar DE, Domchek SM, Nathanson KL, Couch FJ, Kraft P: Risk of Breast Cancer Among Carriers of Pathogenic Variants in Breast Cancer Predisposition Genes Varies by Polygenic Risk Score J Clin Oncol 39 (23): 2564-2573,2021.
Pluta J, Pyle LC, Nead KT, Wilf R, Li M, Mitra N, Weathers B, D'Andrea K, Almstrup K, Anson-Cartwright L, Benitez J, Brown CD, Chanock S, Chen C, Cortessis VK, Ferlin A, Foresta C, Gamulin M, Gietema JA, Grasso C, Greene MH, Grotmol T, Hamilton RJ, Haugen TB, Hauser R, Hildebrandt MAT, Johnson ME, Karlsson R, Kiemeney LA, Lessel D, Lothe RA, Loud JT, Loveday C, Martin-Gimeno P, Meijer C, Nsengimana J, Quinn DI, Rafnar T, Ramdas S, Richiardi L, Skotheim RI, Stefansson K, Turnbull C, Vaughn DJ, Wiklund F, Wu X, Yang D, Zheng T, Wells AD, Grant SFA, Rajpert-De Meyts E, Schwartz SM, Bishop DT, McGlynn KA, Kanetsky PA, Nathanson KL; Testicular Cancer Consortium.: Identification of 22 susceptibility loci associated with testicular germ cell tumors. Nat Commun. 12 (1): 4487,2021.
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