Jennifer Caswell-Jin, MD is a postdoctoral fellow in medical oncology specializing in breast cancer care and research. She received her medical degree from Harvard Medical School in 2010, completed her internal medicine residency at the University of California, San Francisco in 2013, and completed her clinical fellowship in medical oncology at Stanford Hospital & Clinics in 2017.

Honors & Awards

  • Physician Scientist Training Award, Damon Runyon Cancer Research Foundation (2017)
  • Postdoctoral Fellowship Award, Susan G. Komen (2017)
  • ASCO Young Investigator Award, Conquer Cancer Foundation (2017)
  • SCI Fellowship Award, Stanford Cancer Institute (2017)

Professional Education

  • Board Certification, American Board of Internal Medicine (2013)
  • Fellowship, Stanford University School of Medicine, Medical Oncology (2017)
  • Residency, University of California, San Francisco, Internal Medicine (2013)
  • Internship, University of California, San Francisco, Internal Medicine (2011)
  • M.D., Harvard Medical School (2010)
  • A.B., Harvard College, Biological Anthropology (2006)

Stanford Advisors

Research & Scholarship

Current Research and Scholarly Interests

My research is on the translational application of next-generation sequencing technologies to breast cancer care: (1) the value of hereditary cancer genetic panel testing in clinical practice, (2) the mechanisms by which inherited genetic variants lead to breast cancer development, and (3) the analysis of somatic tumor sequencing data to inform understanding of breast tumorigenesis, metastasis, and development of resistance in response to therapeutics.

Lab Affiliations


Graduate and Fellowship Programs

  • Oncology (Fellowship Program)


All Publications

  • Racial/ethnic differences in multiple-gene sequencing results for hereditary cancer risk. Genetics in medicine : official journal of the American College of Medical Genetics Caswell-Jin, J. L., Gupta, T., Hall, E., Petrovchich, I. M., Mills, M. A., Kingham, K. E., Koff, R., Chun, N. M., Levonian, P., Lebensohn, A. P., Ford, J. M., Kurian, A. W. 2017


    PurposeWe examined racial/ethnic differences in the usage and results of germ-line multiple-gene sequencing (MGS) panels to evaluate hereditary cancer risk.MethodsWe collected genetic testing results and clinical information from 1,483 patients who underwent MGS at Stanford University between 1 January 2013 and 31 December 2015.ResultsAsians and Hispanics presented for MGS at younger ages than whites (48 and 47 vs. 55; P?=?5E-16 and 5E-14). Across all panels, the rate of pathogenic variants (15%) did not differ significantly between racial groups. Rates by gene did differ: in particular, a higher percentage of whites than nonwhites carried pathogenic CHEK2 variants (3.8% vs. 1.0%; P?=?0.002). The rate of a variant of uncertain significance (VUS) result was higher in nonwhites than whites (36% vs. 27%; P?=?2E-4). The probability of a VUS increased with increasing number of genes tested; this effect was more pronounced for nonwhites than for whites (1.1% absolute difference in VUS rates testing BRCA1/2 vs. 8% testing 13 genes vs. 14% testing 28 genes), worsening the disparity.ConclusionIn this diverse cohort undergoing MGS testing, pathogenic variant rates were similar between racial/ethnic groups. By contrast, VUS results were more frequent among nonwhites, with potential significance for the impact of MGS testing by race/ethnicity.GENETICS in MEDICINE advance online publication, 27 July 2017; doi:10.1038/gim.2017.96.

    View details for DOI 10.1038/gim.2017.96

    View details for PubMedID 28749474

  • Acute, Unilateral Breast Toxicity From Gemcitabine in the Setting of Thoracic Inlet Obstruction. Journal of oncology practice / American Society of Clinical Oncology Weiskopf, K., Creighton, D., Lew, T., Caswell, J. L., Ouyang, D., Shah, A. T., Hofmann, L. V., Neal, J. W., Telli, M. L. 2016; 12 (8): 763-764

    View details for DOI 10.1200/JOP.2016.014241

    View details for PubMedID 27511721

    View details for PubMedCentralID PMC5012631

  • Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors HUMAN MOLECULAR GENETICS Caswell, J. L., Camarda, R., Zhou, A. Y., Huntsman, S., Hu, D., Brenner, S. E., Zaitlen, N., Goga, A., Ziv, E. 2015; 24 (25): 7421-7431


    Genome-wide association studies have identified over 70 single-nucleotide polymorphisms (SNPs) associated with breast cancer. A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown. We hypothesized that some risk SNPs may regulate alternative splicing. Using RNA-sequencing data from breast tumors and germline genotypes from The Cancer Genome Atlas, we tested the association between each risk SNP genotype and exon-, exon-exon junction- or transcript-specific expression of nearby genes. Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4). We next developed a Bayesian approach to evaluate, for each SNP, the overlap between the signal of association with breast cancer and the signal of association with alternative splicing. At one locus (SRGAP2D), this method eliminated the possibility that the breast cancer risk and the alternate splicing event were due to the same causal SNP. Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay. Our results suggest that the regulation of differential transcript isoform expression is the functional mechanism of some breast cancer risk SNPs and that we can use these associations to identify causal SNPs, target genes and the specific transcripts that may mediate breast cancer risk.

    View details for DOI 10.1093/hmg/ddv432

    View details for Web of Science ID 000368373600021

    View details for PubMedID 26472073

  • Genome-wide association study identifies variants at 16p13 associated with survival in multiple myeloma patients NATURE COMMUNICATIONS Ziv, E., Dean, E., Hu, D., Martino, A., Serie, D., Curtin, K., Campa, D., Aftab, B., Bracci, P., Buda, G., Zhao, Y., Caswell-Jin, J., Diasio, R., Dumontet, C., Dudzinski, M., Fejerman, L., Greenberg, A., Huntsman, S., Jamroziak, K., Jurczyszyn, A., Kumar, S., Atanackovic, D., Glenn, M., Cannon-Albright, L. A., Jones, B., Lee, A., Marques, H., Martin, T., Martinez-Lopez, J., Rajkumar, V., Sainz, J., Vangsted, A. J., Watek, M., Wolf, J., Slager, S., Camp, N. J., Canzian, F., Vachon, C. 2015; 6


    Here we perform the first genome-wide association study (GWAS) of multiple myeloma (MM) survival. In a meta-analysis of 306 MM patients treated at UCSF and 239 patients treated at the Mayo clinic, we find a significant association between SNPs near the gene FOPNL on chromosome 16p13 and survival (rs72773978; P=6 10(-10)). Patients with the minor allele are at increased risk for mortality (HR: 2.65; 95% CI: 1.94-3.58) relative to patients homozygous for the major allele. We replicate the association in the IMMEnSE cohort including 772 patients, and a University of Utah cohort including 318 patients (rs72773978 P=0.044). Using publicly available data, we find that the minor allele was associated with increased expression of FOPNL and increased expression of FOPNL was associated with higher expression of centrosomal genes and with shorter survival. Polymorphisms at the FOPNL locus are associated with survival among MM patients.

    View details for DOI 10.1038/ncomms8539

    View details for Web of Science ID 000358852600004

    View details for PubMedID 26198393

  • Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25 NATURE COMMUNICATIONS Fejerman, L., Ahmadiyeh, N., Hu, D., Huntsman, S., Beckman, K. B., Caswell, J. L., Tsung, K., John, E. M., Torres-Mejia, G., Carvajal-Carmona, L., Echeverry, M. M., Tuazon, A. M., Ramirez, C., Gignoux, C. R., Eng, C., Gonzalez-Burchard, E., Henderson, B., Le Marchand, L., Kooperberg, C., Hou, L., Agalliu, I., Kraft, P., Lindstroem, S., Perez-Stable, E. J., Haiman, C. A., Ziv, E. 2014; 5


    The genetic contributions to breast cancer development among Latinas are not well understood. Here we carry out a genome-wide association study of breast cancer in Latinas and identify a genome-wide significant risk variant, located 5' of the Estrogen Receptor 1 gene (ESR1; 6q25 region). The minor allele for this variant is strongly protective (rs140068132: odds ratio (OR) 0.60, 95% confidence interval (CI) 0.53-0.67, P=9 10(-18)), originates from Indigenous Americans and is uncorrelated with previously reported risk variants at 6q25. The association is stronger for oestrogen receptor-negative disease (OR 0.34, 95% CI 0.21-0.54) than oestrogen receptor-positive disease (OR 0.63, 95% CI 0.49-0.80; P heterogeneity=0.01) and is also associated with mammographic breast density, a strong risk factor for breast cancer (P=0.001). rs140068132 is located within several transcription factor-binding sites and electrophoretic mobility shift assays with MCF-7 nuclear protein demonstrate differential binding of the G/A alleles at this locus. These results highlight the importance of conducting research in diverse populations.

    View details for DOI 10.1038/ncomms6260

    View details for Web of Science ID 000343985400009

    View details for PubMedCentralID PMC4204111

  • High mammographic density in women of Ashkenazi Jewish descent BREAST CANCER RESEARCH Caswell, J. L., Kerlikowske, K., Shepherd, J. A., Cummings, S. R., Hu, D., Huntsman, S., Ziv, E. 2013; 15 (3)


    Percent mammographic density (PMD) adjusted for age and body mass index is one of the strongest risk factors for breast cancer and is known to be approximately 60% heritable. Here we report a finding of an association between genetic ancestry and adjusted PMD.We selected self-identified Caucasian women in the California Pacific Medical Center Research Institute Cohort whose screening mammograms placed them in the top or bottom quintiles of age-adjusted and body mass index-adjusted PMD. Our final dataset included 474 women with the highest adjusted PMD and 469 with the lowest genotyped on the Illumina 1 M platform. Principal component analysis (PCA) and identity-by-descent analyses allowed us to infer the women's genetic ancestry and correlate it with adjusted PMD.Women of Ashkenazi Jewish ancestry, as defined by the first principal component of PCA and identity-by-descent analyses, represented approximately 15% of the sample. Ashkenazi Jewish ancestry, defined by the first principal component of PCA, was associated with higher adjusted PMD (P = 0.004). Using multivariate regression to adjust for epidemiologic factors associated with PMD, including age at parity and use of postmenopausal hormone therapy, did not attenuate the association.Women of Ashkenazi Jewish ancestry, based on genetic analysis, are more likely to have high age-adjusted and body mass index-adjusted PMD. Ashkenazi Jews may have a unique set of genetic variants or environmental risk factors that increase mammographic density.

    View details for DOI 10.1186/bcr3424

    View details for Web of Science ID 000328937600004

    View details for PubMedID 23668689

  • 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ahmadiyeh, N., Pomerantz, M. M., Grisanzio, C., Herman, P., Jia, L., Almendro, V., He, H. H., Brown, M., Liu, X. S., Davis, M., Caswell, J. L., Beckwith, C. A., Hills, A., MacConaill, L., Coetzee, G. A., Regan, M. M., Freedman, M. L. 2010; 107 (21): 9742-9746


    The 8q24 gene desert contains risk loci for multiple epithelial cancers, including colon, breast, and prostate. Recent evidence suggests these risk loci contain enhancers. In this study, data are presented showing that each risk locus bears epigenetic marks consistent with enhancer elements and forms a long-range chromatin loop with the MYC proto-oncogene located several hundred kilobases telomeric and that these interactions are tissue-specific. We therefore propose that the 8q24 risk loci operate through a common mechanism-as tissue-specific enhancers of MYC.

    View details for DOI 10.1073/pnas.0910668107

    View details for Web of Science ID 000278054700049

    View details for PubMedID 20453196

  • Analysis of chimpanzee history based on genome sequence alignments PLOS GENETICS Caswell, J. L., Mallick, S., Richter, D. J., Neubauer, J., Gnerre, C. S., Gnerre, S., Reich, D. 2008; 4 (4)


    Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated approximately 1,290,000 years ago, western and other common chimpanzees approximately 510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5-7 million years ago when the ancestors of humans separated from those of the chimpanzees.

    View details for DOI 10.1371/journal.pgen.1000057

    View details for Web of Science ID 000255407400011

    View details for PubMedID 18421364

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