Marina Corines

A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia

Somatic alterations of the lymphoid transcription factor gene PAX5 (also known as BSAP) are a hallmark of B cell precursor acute lymphoblastic leukemia (B-ALL), but inherited mutations of PAX5 have not previously been described. Here we report a new heterozygous germline variant, c.547G>A (p.Gly183Ser), affecting the octapeptide domain of PAX5 that was found to segregate with disease in two unrelated kindreds with autosomal dominant B-ALL. Leukemic cells from all affected individuals in both families exhibited 9p deletion, with loss of heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss harbored somatic PAX5 substitutions affecting Gly183. Functional and gene expression analysis of the PAX5 mutation demonstrated that it had significantly reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B cell ALL and implicate PAX5 in a new syndrome of susceptibility to pre-B cell neoplasia.

An analysis of the association between prostate cancer risk loci, PSA levels, disease aggressiveness and disease-specific mortality

Background:Genome-wide association studies have identified multiple single-nucleotide polymorphsims (SNPs) associated with prostate cancer (PCa). Although these SNPs have been clearly associated with disease risk, their relationship with clinical outcomes is less clear. Our aim was to assess the frequency of known PCa susceptibility alleles within a single institution ascertainment and to correlate risk alleles with disease-specific outcomes.Methods:We genotyped 1354 individuals treated for localised PCa between June 1988 and December 2007. Blood samples were prospectively collected and de-identified before being genotyped and matched to phenotypic data. We investigated associations between 61 SNPs and disease-specific end points using multivariable analysis and also determined if SNPs were associated with PSA at diagnosis.Results:Seven SNPs showed associations on multivariable analysis (P<0.05), rs13385191 with both biochemical recurrence (BR) and castrate metastasis (CM), rs339331 (BR), rs1894292, rs17178655 and rs11067228 (CM), and rs11902236 and rs4857841 PCa-specific mortality. After applying a Bonferroni correction for number of SNPs (P<0.0008), the only persistent significant association was between rs17632542 (KLK3) and PSA levels at diagnosis (P=1.4 × 10−5).Conclusions:We confirmed that rs17632542 in KLK3 is associated with PSA at diagnosis. No significant association was seen between loci and disease-specific end points when accounting for multiple testing. This provides further evidence that known PCa risk SNPs do not predict likelihood of disease progression.

Genome sequencing of multiple primary tumors reveals a novel PALB2 variant

Introduction PALB2 (partner and localizer of BRCA2) has been implicated in hereditary breast cancer susceptibility, with estimates of breast cancer risk up to 91% (95% CI, 44% to 100%) to age 70 years for particular mutations. Germline mutations in PALB2 have also been identified in individuals with pancreatic cancer and ovarian carcinoma, both with and without familial breast cancer, suggesting a role in susceptibility to breast and ovarian cancer. PALB2 acts in the double-strand DNA break repair pathway recruiting RAD51 and BRCA2 to DNA breaks via its WD40 domain. Biallelic germline mutations cause Fanconi anemia, complementation group N(FANCN). Pathogenic germline variants of PALB2 causing loss of normal function may be substitutions or insertions/ deletions. Tumors in germline PALB2 mutation carriers show loss of the wild-type allele consistent with a tumor suppressor function. Structural variants deleting or duplicating multiple exons of PALB2 have been reported in association with familial breast cancer and in FANCN, and founder and recurrent mutations in PALB2 have been identified in several populations.

Abstract 3282: Determination of cancer susceptibility in probands with breast and ovarian cancer

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Germline mutations of BRCA1 and BRCA2 underlie joint susceptibility to breast and ovarian cancers, but do not account for all cases. Genome wide association studies show little overlap between common variants associated with breast and ovarian cancer susceptibility, whereas rare variants in genes initially identified as breast cancer susceptibility genes also confer susceptibility to ovarian cancer cases, unselected for breast cancer. Ovarian and breast tumors also are observed in Peutz-Jeghers and possibly in Lynch syndrome. To further elucidate rare germline susceptibilities for breast and ovarian cancer, we have ascertained a unique cohort of 90 BRCA1/2-negative probands with a personal history of breast cancer and ovarian/fallopian tube/peritoneal cancer, unselected for family history. Cases are from the clinical genetics services of Memorial Sloan-Kettering Cancer Center and University of Pennsylvania. Analysis is ongoing using both targeted and exome sequencing approaches. Germline DNA of 69 cases will be subjected to whole exome sequencing. A total of 21 additional cases will undergo targeted sequencing for 28 genes (8 cases) and an extended panel of 54 genes (13 cases). The majority of ovarian cancers are high-grade serous epithelial ovarian carcinoma (n=51), in combination with invasive ductal or DCIS (n=36), invasive lobular (n=4), or unspecified (n=11) breast cancers. The remaining ovarian subgroups comprise other epithelial subtypes; endometrioid (n=9), clear cell (n=3), mucinous and low-grade serous (n=3) and non-epithelial (n=4) or unclassified (n=20), in combination with invasive ductal or DCIS (n=21), invasive lobular (n=5) or unspecified (n=13) breast cancers. Preliminary analysis of the targeted set of genes in 69 cases, reveals 43 predicted pathogenic coding or splice site variants; 17 of which are within PALB2, MSH2, MSH6, BARD1, FANCE, CDKN2A, TP53, SETD2, SIRT1, BRIP1, RAD50, and RAD51D and are not seen in dbSNP138, 1000 Genomes or Exome Variant Server ESP6500 and 26 variants with reported frequencies in MUTYH, MSH6, MLH1, FAM175A, RAD50, UIMC1, JARID2, PHF3, SIRT1, MRE11A, ATM, BRCA2, TP53BP1, CDH1, RAD51D, BRCA1, BABAM1 of less than 1% allele frequency in public databases. Analysis of these variants across and within histologic subtypes is being undertaken to look for specific genotype-phenotype correlations. Analysis of novel candidate genes and pathways by co-segregation, functional analysis, as well as external replication is underway to determine whether shared rare variants, mutated genes, or altered pathways confer cancer susceptibility in this cohort. Germline susceptibility to breast and ovarian cancer is heterogenous and remains a critical research and clinical question. Improved understanding of the susceptibility genetics will allow further examination of the utility of targeted cancer prevention strategies in those who are found to be at risk. Citation Format: Kasmintan A. Schrader, Kara N. Maxwell, Joseph Vijai, Steven Hart, Tinu Thomas, Bradley Wubbenhorst, Lucia Guidugli, Robert Klein, Marina Corines, Liying Zhang, Susan Neuhausen, Jeffrey Weitzel, Namrata Gupta, Larry Norton, Clifford Hudis, Gad Getz, Mark Daly, Steven Lipkin, David Altshuler, Fergus Couch, Katherine Nathanson, Kenneth Offit. Determination of cancer susceptibility in probands with breast and ovarian cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3282. doi:10.1158/1538-7445.AM2014-3282