Search

ClinVar variant interpretations from May 2019 for variants identified in discovery cohorts

Germline loss-of-function mutations in BRCA1 interacting protein C-terminal helicase 1 (BRIP1) are associated with ovarian carcinoma and may also contribute to breast cancer risk, particularly among patients who develop disease at an early age. Normal BRIP1 activity is required for DNA interstrand cross-link (ICL) repair and is thus central to the maintenance of genome stability. Although pathogenic mutations have been identified in BRIP1, genetic testing more often reveals missense variants, for which the impact on molecular function and subsequent roles in cancer risk are uncertain. Next-generation sequencing of germline DNA in 2,160 early-onset breast cancer and 1,199 patients with ovarian cancer revealed nearly 2% of patients carry a very rare missense variant (minor allele frequency < 0.0001) in BRIP1. This is 3-fold higher than the frequency of all rare BRIP1 missense alleles reported in more than 60,000 individuals of the general population (P < 0.0001, χ2 test). Using CRISPR-Cas9 gene editing technology and rescue assays, we functionally characterized 20 of these missense variants, focusing on the altered protein's ability to repair ICL damage. A total of 75% of the characterized variants rendered the protein hypomorph or null. In a clinical cohort of >117,000 patients with breast and ovarian cancer who underwent panel testing, the combined OR associated with BRIP1 hypomorph or null missense carriers compared with the general population was 2.30 (95% confidence interval, 1.60–3.30; P < 0.0001). These findings suggest that novel missense variants within the helicase domain of BRIP1 may confer risk for both breast and ovarian cancer and highlight the importance of functional testing for additional variants.Significance:Functional characterization of rare variants of uncertain significance in BRIP1 revealed that 75% demonstrate loss-of-function activity, suggesting rare missense alleles in BRIP1 confer risk for both breast and ovarian cancer.

Supplementary methods; FS1: BRIP1 nonsense and frameshift mutations; FS2: BRIP1 expression in CRISPR cell lines; FS3: hydroxyurea and TMPyP4 challenge; FS4: HEK293TN CRISPR cell lines; FS5: HeLa stable clone rescues; FS6: Transient rescue screening assay; FS7: Degradation of missense mutant proteins; TS1: List of BRIP1 missense variants identified in cohorts

Implicit racial bias in healthcare settings can impact delivery of patient care. Exploration of this bias is necessary to improve patient experiences. We sought to understand implicit racial bias among graduates of accredited genetic counseling programs in the United States and Canada in the class of 2020 as they enter the genetics workforce and assess how this bias is associated with training and life experiences. Implicit racial bias was quantified through use of the Black-White Implicit Association Test (BW-IAT). Participants also completed an online survey focused on didactic and clinical training and personal experiences with diverse populations. Participants (n = 100) were majority White (88%), and 44% demonstrated an implicit bias favoring White individuals. Respondents reported a lack of interaction with Black healthcare professionals during their training. A concerning proportion (38%) reported experiencing or witnessing racial insensitivity perpetrated by genetic counselors or physicians in supervisory roles. Graduates reported diversity coursework as significantly less effective overall than other general genetic counseling coursework. This study reveals prevalence of implicit racial bias among genetic counselor graduates, lack of exposure to diverse populations within and outside of graduate training, and concerns regarding racial insensitivity and effectiveness of didactic and clinical genetic counseling training. Employers and program directors should implement revisions to ongoing training and graduate curriculum with consideration of these findings.

Germline loss-of-function mutations in BRCA1 interacting protein C-terminal helicase 1 (BRIP1) are associated with ovarian carcinoma and may also contribute to breast cancer risk, particularly among patients who develop disease at an early age. Normal BRIP1 activity is required for DNA interstrand cross-link (ICL) repair and is thus central to the maintenance of genome stability. Although pathogenic mutations have been identified in BRIP1, genetic testing more often reveals missense variants, for which the impact on molecular function and subsequent roles in cancer risk are uncertain. Next-generation sequencing of germline DNA in 2,160 early-onset breast cancer and 1,199 patients with ovarian cancer revealed nearly 2% of patients carry a very rare missense variant (minor allele frequency < 0.0001) in BRIP1. This is 3-fold higher than the frequency of all rare BRIP1 missense alleles reported in more than 60,000 individuals of the general population (P < 0.0001, χ2 test). Using CRISPR-Cas9 gene editing technology and rescue assays, we functionally characterized 20 of these missense variants, focusing on the altered protein's ability to repair ICL damage. A total of 75% of the characterized variants rendered the protein hypomorph or null. In a clinical cohort of >117,000 patients with breast and ovarian cancer who underwent panel testing, the combined OR associated with BRIP1 hypomorph or null missense carriers compared with the general population was 2.30 (95% confidence interval, 1.60–3.30; P < 0.0001). These findings suggest that novel missense variants within the helicase domain of BRIP1 may confer risk for both breast and ovarian cancer and highlight the importance of functional testing for additional variants. Significance: Functional characterization of rare variants of uncertain significance in BRIP1 revealed that 75% demonstrate loss-of-function activity, suggesting rare missense alleles in BRIP1 confer risk for both breast and ovarian cancer.

Information-seeking models typically focus on information-seeking behavior, that is, an individual’s interest in information because their current level is perceived to be insufficient. In the context of genetic risk information (GRI), however, information insufficiency is difficult to measure and thus can limit understanding of information behavior in the context of GRI. We propose that an individual’s need for information might be a more direct and conceptually clearer alternative to predicting their information-seeking behavior. To test this hypothesis, this study investigates the extent to which previously identified factors affecting interest in GRI are also predictors of need for GRI among women diagnosed with breast cancer at the age of 40 or younger (N = 1,069). As hypothesized, there was a positive association between interest in, and need for, GRI. Furthermore, hypothesized factors of numeracy, information orientation, and genetic knowledge, were significant predictors of increased interest in, and need for, GRI. In contrast, hypothesized factors of genetic worry and genetic causal belief predicted increased interest in GRI only, while genetic self-efficacy predicted increased need for GRI only. As hypothesized, BRCA mutation status significantly moderated associations between informational norm and both interest in, and need for, GRI. Collectively, the findings support inclusion of need for GRI in theoretical information-seeking models in the context of genomic risk.

Germline loss-of-function mutations in BRIP1 are associated with ovarian carcinoma and may also contribute to breast cancer risk, particularly among patients who develop disease at an early age. Normal BRIP1 activity is required for DNA interstrand crosslink repair, and is thus central to the maintenance of genome stability. Although pathogenic mutations have been identified in BRIP1, genetic testing more often reveals missense variants for which the impact on molecular function and subsequent roles in cancer risk are uncertain. Next generation sequencing of germline DNA in 2,160 early-onset breast cancer and 1,199 ovarian cancer patients revealed nearly 2% of patients carry a very rare missense variant (MAF117,000 breast and ovarian cancer patients who underwent panel testing, the combined odds ratio associated with BRIP1 hypomorph or null missense carriers compared to the general population was 2.30 (95%CI=1.60-3.30, p

Background The increasing use of genome sequencing with patients raises a critical communication challenge: return of secondary findings. While the issue of what sequencing results should be returned to patients has been examined, much less attention has been paid to developing strategies to return these results in ways that meet patients' needs and preferences. To address this, we investigated delivery preferences (i.e., who, how, when) for individual genome sequencing results among women diagnosed with breast cancer at age 40 or younger. Methods We conducted 60 semistructured, in‐person individual interviews to examine preferences for the return of different types of genome sequencing results and the reasons underlying these preferences. Two coders independently coded interview transcripts; analysis was conducted using NVivo 10. Results The major findings from the study were that: (1) many participants wanted sequencing results as soon as possible, even at the time of breast cancer diagnosis; (2) participants wanted an opportunity for an in‐person discussion of results; and (3) they put less emphasis on the type of person delivering results than on the knowledge and communicative skills of that person. Participants also emphasized the importance of a results return process tailored to a patient's individual circumstances and one that she has a voice in determining. Conclusions A critical goal for future transdisciplinary research including clinicians, patients, and communication researchers may be to develop decision‐making processes to help patients make decisions about how they would like various sequencing results returned., While the issue of what genome sequencing results should be returned to patients has been examined, much less attention has been paid to developing strategies to return these results in ways that meet patients' needs and preferences. To address this, we investigated delivery preferences (i.e., who, how, when) for individual genome sequencing results among women diagnosed with breast cancer at age 40 or younger. The major findings from the study were that: (1) many participants wanted sequencing results as soon as possible, even at the time of breast cancer diagnosis; (2) participants wanted an opportunity for an in‐person discussion of results; and (3) they put less emphasis on the type of person delivering results than on the knowledge and communicative skills of that person.

We investigated what information women diagnosed with breast cancer at a young age would want to learn when genome sequencing results are returned. We conducted 60 semi-structured interviews with women diagnosed with breast cancer at age 40 or younger. We examined what specific information participants would want to learn across result types and for each type of result, as well as how much information they would want. Genome sequencing was not offered to participants as part of the study. Two coders independently coded interview transcripts; analysis was conducted using NVivo10. Across result types, participants wanted to learn about health implications, risk and prevalence in quantitative terms, causes of variants, and causes of diseases. Participants wanted to learn actionable information for variants affecting risk of preventable or treatable disease, medication response, and carrier status. The amount of desired information differed for variants affecting risk of unpreventable or untreatable disease, with uncertain significance, and not health-related. Women diagnosed with breast cancer at a young age recognize the value of genome sequencing results in identifying potential causes and effective treatments and expressed interest in using the information to help relatives and to further understand their other health risks. Our findings can inform the development of effective feedback strategies for genome sequencing that meet patients’ information needs and preferences.

Next-generation sequencing has revolutionized cancer genetics, but accurately detecting mutations in repetitive DNA sequences, especially mononucleotide runs, remains a challenge. This is a particular concern for tumors with defective mismatch repair (MMR) that accumulate strand-slippage mutations. We developed MonoSeq to improve indel mutation detection in mononucleotide runs, and used MonoSeq to investigate strand-slippage mutations in endometrial cancers, a tumor type that has frequent loss of MMR. We performed extensive Sanger sequencing to validate both clonal and subclonal MonoSeq mutation calls. Eighty-one regions containing mononucleotide runs were sequenced in 540 primary endometrial cancers (223 with defective MMR). Our analyses revealed that the overall mutation rate in MMR-deficient tumors was 20-30-fold higher than in MMR-normal tumors. MonoSeq analysis identified several previously unreported mutations, including a novel hotspot in an A7 run in the terminal exon of ARID5B.The ARID5B indel mutations were seen in both MMR-deficient and MMR-normal tumors, suggesting biologic selection. The analysis of tumor mRNAs revealed the presence of mutant transcripts that could result in translation of neopeptides. Improved detection of mononucleotide run strand-slippage mutations has clear implications for comprehensive mutation detection in tumors with defective MMR. Indel frameshift mutations and the resultant antigenic peptides could help guide immunotherapy strategies.

Genetic test results have medical implications beyond the patient that extend to biological family members. We examined psychosocial and clinical factors associated with communication of genetic test results within families. Women (N = 1080) diagnosed with breast cancer at age 40 or younger completed an online survey; 920 women that reported prior cancer genetic testing were included in analysis. We examined the proportion of immediate family members to whom they communicated genetic test results, and built multivariable regression models to examine clinical and psychosocial variables associated with the proportion score. Participants were most likely to communicate test results to their mother (83 %) and least likely to their son (45 %). Participants who carried a BRCA mutation (OR = 1.34; 95 % CI = 1.06, 1.70), had higher interest in genomic information (OR = 1.55; 95 % CI = 1.26, 1.91) and lower genetic worry (OR = 0.91; 95 % CI = 0.86, 0.96) communicated genetic test results to a greater proportion of their immediate family members. Participants with a BRCA1/2 mutation shared their genetic test results with more male family members (OR = 1.72; 95 % CI = 1.02, 2.89). Our findings suggest that patients with high worry about genetic risks, low interest in genomic information, or receive a negative genetic test result will likely need additional support to encourage family communication.

Younger age diagnosis of breast cancer is a predictor of adverse outcome. Here, we evaluate prognostic factors in young women with locally advanced breast cancer (LABC). We present a retrospective review of 104 patients younger than 40 years with LABC treated with surgery, radiotherapy (RT), and chemotherapy from 2003 to 2014. Patient‐, tumor‐, and treatment‐related factors important for overall survival (OS), local/regional recurrence (LRR), distant metastasis (DM), and recurrence‐free survival (RFS) were evaluated. Mean age at diagnosis was 34 years (23–39 years) with a median follow‐up of 47 months (8–138 months). Breast‐conserving surgery was performed in 27%. Axillary lymph node dissection was performed in 85%. Sixty percent of patients received neoadjuvant chemotherapy with 19% achieving pathologic complete response (pCR), and 61% downstaged. Lymph node positivity was present in 91% and lymphovascular space invasion (LVSI) in 35%. Thirty‐two percent of patients had triple negative tumors (TN, ER‐/PR‐/HER2 nonamplified). Four‐year OS and RFS was 84% and 71%, respectively. Factors associated with worse OS on multivariate analysis include TN status, LVSI, and number of positive lymph nodes. LVSI was also associated with DM and LRR, as well as worse RFS. Downstaging was associated with improved 4 year RFS in patients receiving neoadjuvant chemotherapy (74% vs. 38%, P = 0.002). With high risks of recurrence and inferior OS compared to older women, breast cancer in young women can be difficult to treat. Among additional factors, presence of LVSI and lack of downstaging portends a particularly worse prognosis.

While experts have made recommendations, information is needed regarding what genome sequencing results patients would want returned. We investigated what results women diagnosed with breast cancer at a young age would want returned and why. We conducted 60 semi-structured, in-person individual interviews with women diagnosed with breast cancer at age 40 or younger. We examined interest in six types of incidental findings and reasons for interest or disinterest in each type. Two coders independently coded interview transcripts; analysis was conducted using NVivo 10. Most participants were at least somewhat interested in all six result types, but strongest interest was in actionable results (i.e. variants affecting risk of a preventable or treatable disease and treatment response). Reasons for interest varied between different result types. Some participants were not interested or ambivalent about results not seen as currently actionable. Participants wanted to be able to choose what results are returned. Participants distinguished between types of individual genome sequencing results, with different reasons for wanting different types of information. The findings suggest that a focus on actionable results can be a common ground for all stakeholders in developing a policy for returning individual genome sequencing results.

Estrogen receptor (ER)-negative breast cancer shows a higher incidence in women of African ancestry compared to women of European ancestry. In search of common risk alleles for ER-negative breast cancer, we combined genome-wide association study (GWAS) data from women of African ancestry (1,004 ER-negative cases and 2,745 controls) and European ancestry (1,718 ER-negative cases and 3,670 controls), with replication testing conducted in an additional 2,292 ER-negative cases and 16,901 controls of European ancestry. We identified a common risk variant for ER-negative breast cancer at the TERT-CLPTM1L locus on chromosome 5p15 (rs10069690: per-allele odds ratio (OR) = 1.18 per allele, P = 1.0 × 10(-10)). The variant was also significantly associated with triple-negative (ER-negative, progesterone receptor (PR)-negative and human epidermal growth factor-2 (HER2)-negative) breast cancer (OR = 1.25, P = 1.1 × 10(-9)), particularly in younger women (

Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumor progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumor, a brain metastasis, and a xenograft derived from the primary tumor. The metastasis contained two de novo mutations and a large deletion not present in the primary tumor, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumor mutations, and displayed a mutation enrichment pattern that paralleled the metastasis (16 of 20 genes). Two overlapping large deletions, encompassing CTNNA1, were present in all three tumor samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared to the primary tumor suggest that secondary tumors may arise from a minority of cells within the primary.

Lay Summary Acute myeloid leukemia is a highly malignant hematopoietic tumor that affects about 13,000 adults yearly in the United States. The treatment of this disease has changed little in the past two decades, since most of the genetic events that initiate the disease remain undiscovered. Whole genome sequencing is now possible at a reasonable cost and timeframe to utilize this approach for unbiased discovery of tumor-specific somatic mutations that alter the protein-coding genes. Here we show the results obtained by sequencing a typical acute myeloid leukemia genome and its matched normal counterpart, obtained from the patient’s skin. We discovered 10 genes with acquired mutations; two were previously described mutations thought to contribute to tumor progression, and 8 were novel mutations present in virtually all tumor cells at presentation and relapse, whose function is not yet known. Our study establishes whole genome sequencing as an unbiased method for discovering initiating mutations in cancer genomes, and for identifying novel genes that may respond to targeted therapies. We used massively parallel sequencing technology to sequence the genomic DNA of tumor and normal skin cells obtained from a patient with a typical presentation of FAB M1 Acute Myeloid Leukemia (AML) with normal cytogenetics. 32.7-fold ‘haploid’ coverage (98 billion bases) was obtained for the tumor genome, and 13.9-fold coverage (41.8 billion bases) was obtained for the normal sample. Of 2,647,695 well-supported Single Nucleotide Variants (SNVs) found in the tumor genome, 2,588,486 (97.7%) also were detected in the patient’s skin genome, limiting the number of variants that required further study. For the purposes of this initial study, we restricted our downstream analysis to the coding sequences of annotated genes: we found only eight heterozygous, non-synonymous somatic SNVs in the entire genome. All were novel, including mutations in protocadherin/cadherin family members (CDH24 and PCLKC), G-protein coupled receptors (GPR123 and EBI2), a protein phosphatase (PTPRT), a potential guanine nucleotide exchange factor (KNDC1), a peptide/drug transporter (SLC15A1), and a glutamate receptor gene (GRINL1B). We also detected previously described, recurrent somatic insertions in the FLT3 and NPM1 genes. Based on deep readcount data, we determined that all of these mutations (except FLT3) were present in nearly all tumor cells at presentation, and again at relapse 11 months later, suggesting that the patient had a single dominant clone containing all of the mutations. These results demonstrate the power of whole genome sequencing to discover novel cancer-associated mutations.

Telomerase, which maintains the ends of chromosomes, consists of two core components, the telomerase reverse transcriptase (TERT) and the telomerase RNA (TERC). Haploinsufficiency for TERC or TERT leads to progressive telomere shortening and autosomal dominant dyskeratosis congenita (DC). The clinical manifestations of autosomal dominant DC are thought to occur when telomeres become critically short, but the rate of telomere shortening in this condition is unknown. Here, we investigated the consequences of de novo TERT gene deletions in a large cohort of individuals with 5p– syndrome. The study group included 41 individuals in which the chromosome deletion resulted in loss of one copy of the TERT gene at 5p15.33. Telomere length in peripheral blood cells from these individuals, although within the normal range, was on average shorter than in normal controls. The shortening was more significant in older individuals suggesting an accelerated age-dependent shortening. In contrast, individuals with autosomal dominant DC due to an inherited TERC gene deletion had very short telomeres, and the telomeres were equally short regardless of the age. Although some individuals with 5p– syndrome showed clinical features that were reminiscent of autosomal dominant DC, these features did not correlate with telomere length, suggesting that these were not caused by critically short telomeres. We conclude that a TERT gene deletion leads to slightly shorter telomeres within one generation. However, our results suggest that several generations of TERT haploinsufficiency are needed to produce the very short telomeres seen in patients with DC.

A variety of neutral serine proteases are important for the effector functions of immune cells. The neutrophil-derived serine proteases cathepsin G and neutrophil elastase are implicated in the host defense against invading bacterial and fungal pathogens. Likewise, the cytotoxic lymphocyte and NK cell granule-associated granzymes A and B are important for the elimination of virus-infected cells. The activation of many of these serine proteases depends on the N-terminal processing activity of the lysosomal cysteine protease cathepsin C/dipeptidyl peptidase I (DPPI). Although mice deficient in DPPI have defects in serine protease activation in multiple cellular compartments, the role of DPPI for human serine protease activation is largely undefined. Papillon-Lefèvre syndrome (PLS) is a rare autosomal recessive disease associated with loss-of-function mutations in the DPPI gene locus. In this study, we established that the loss of DPPI activity is associated with severe reduction in the activity and stability of neutrophil-derived serine proteases. Surprisingly, patients with PLS retain significant granzyme activities in a cytotoxic lymphocyte compartment (lymphokine-activated killer) and have normal lymphokine-activated killer-mediated cytotoxicity against K562 cells. Neutrophils from patients with PLS do not uniformly have a defect in their ability to kill Staphylococcus aureus and Escherichia coli, suggesting that serine proteases do not represent the major mechanism used by human neutrophils for killing common bacteria. Therefore, this study defines the consequences of DPPI deficiency for the activation of several immune cell serine proteases in humans, and provides a molecular explanation for the lack of a generalized T cell immunodeficiency phenotype in patients with PLS.

Physicians have been inundated with news as to how advances in genetics, and developments in genetic technology, will alter their daily practice. While it is true the complexity of the underlying genetic basis for colorectal cancer predisposition is slowly being recognized, the impact of these advances has been limited in the clinical setting. Cancer genetics assessment has yet to become a routine clinical service offered in the management of people with, or at-risk for, colorectal cancer. As the clinical impact of genetic medicine expands, the need for a multidisciplinary approach, including clinical genetics assessment, takes on an even greater significance. This article serves to revisit the role of genetics assessment in the care of families with an increased family-based cancer risk. Three practical cases are used to demonstrate this role and to discuss issues associated with hereditary gastrointestinal cancer syndromes.

We have characterized the molecular basis of beta-hexosaminidase A (HEX A) deficiency in a patient ascertained through an ophthalmologic examination that revealed cherry red spots on his retina. The absence of neurological deficit in this child until 3(3)/(4) years of age indicated residual HEX A must be present. Three HEXA mutations, 10T > C (S4P) and 972T > A (V324V) on the maternal allele, and 1A > T (M1L) on the paternal allele were identified. The effects of the amino acid substitutions on HEX A expressed in COS-7 cells were analyzed; as expected, no HEX A activity was associated with the M1L mutation but surprisingly, the S4P mutation resulted in 59% of the HEX A activity expressed by the wild type cDNA. The effect of the S4P change was much less than that of another HEXA mutation, G269S, associated with an adult onset form Of G(M2) gangliosidosis. This indicated that the S4P change was not the cause of disease and suggested that one of the mutations on the maternal allele, 10T > C or 972T > A, had its effect at the mRNA level. This was confirmed by Northern blot analysis that showed only 7% of the normal level of HEXA mRNA in proband fibroblasts. Analysis of the residual mRNA by RT/PCR and sequencing revealed normal transcripts from both the maternal and paternal allele, as well as a low abundance aberrant transcript from the maternal allele. Sequencing of this aberrant transcript revealed a new exon 8 donor site created by the 972T > A mutation that resulted in a 17 bp deletion and destabilization of the resulting abnormal transcript. The remaining normal mRNA produced from the 972T > A allele must account for the delayed onset of clinical symptoms in this child. (C) 2004 Wiley-Liss, Inc.

Loss of DNA mismatch repair occurs in a variety of malignancies and is associated with genome-wide instability of microsatellite repeats, a molecular phenotype referred to as microsatellite instability (MSI). MSI is a consistent feature of colorectal and endometrial tumors from patients with hereditary non-polyposis colorectal cancer (HNPCC). Sporadic colorectal and endometrial cancers that exhibit MSI frequently have methylation of the MLH1 promoter. We undertook a detailed family and medical history study to compare family cancer risk for women with MSI-positive and -negative endometrial cancers. The MLH1 promoter methylation status was determined for all cancers. Family histories were developed for 80 probands (40 with MSI-positive and 40 with MSI-negative tumors). The numbers of reported cancers in first- and second-degree relatives of the 2 groups were similar. There was a modest increase in familial cancer clustering for MSI-positive probands. When MSI-positive tumors were subclassified according to MLH1 promoter methylation, a clear association between methylation status and familial cancer risk was evident. Women with MSI-positive endometrial cancers in which the MLH1 promoter was unmethylated had a 7-fold relative risk (RR) of demonstrating familial clustering of cancers [RR 7.07 (95% confidence interval 2.29-21.81)]. The women with MSI-positive, MLH1-unmethylated tumors were significantly younger than the rest of the study population (56.1 years vs. 65.4, p < or = 0.01). Age of onset and tumor MSI not associated with MLH1 promoter methylation may point to women with a genetic susceptibility to malignancies.

Neuroectodermal melanolysosomal disease, also known as Elejalde syndrome, is a rare syndrome characterized by silvery hair, pigment abnormalities, and profound central nervous system dysfunction. It is similar to the Chediak-Higashi and Griscelli syndromes, although these syndromes are associated with severe immunologic dysfunction. We report on a 12-year-old male with Elejalde syndrome and compare the Elejalde, Chediak-Higashi, and Griscelli syndromes.

The microsatellite instability that is a feature of tumors in patients with hereditary nonpolyposis colorectal cancer (HNPCC) is a consequence of defective DNA mismatch repair. Mutations in the DNA mismatch repair genes MSH2 and MLH1 may account for up to 90% of HNPCC kindreds. Microsatellite instability is also seen in 10-16% of sporadic colorectal cancers. A limited number of MSH2 and MLH1 mutations have been described for sporadic colorectal cancers. In this study, we screened 12 primary sporadic colorectal cancers with microsatellite instability for mutations in MSH2 and MLH1 by using reverse transcription-polymerase chain reaction (RT-PCR) and single-strand-conformation-variant (SSCV) analysis. Eight mutations were identified in six tumors. One mutation in MLH1 was found to be present in the patient's germline DNA. Four tumors had somatic mutations in MLH1, and, in two of these tumors, two different mutations were identified. A single tumor had a somatic MSH2 mutation. Our observations suggest that MLH1 is mutated more frequently than MSH2 in sporadic colorectal cancers with microsatellite instability.

Triple-negative (TN) breast cancer is an aggressive subtype of breast cancer associated with a unique set of epidemiologic and genetic risk factors. We conducted a two-stage genome-wide association study of TN breast cancer (stage 1: 1529 TN cases, 3399 controls; stage 2: 2148 cases, 1309 controls) to identify loci that influence TN breast cancer risk. Variants in the 19p13.1 and PTHLH loci showed genome-wide significant associations (P < 5 × 10(-) (8)) in stage 1 and 2 combined. Results also suggested a substantial enrichment of significantly associated variants among the single nucleotide polymorphisms (SNPs) analyzed in stage 2. Variants from 25 of 74 known breast cancer susceptibility loci were also associated with risk of TN breast cancer (P < 0.05). Associations with TN breast cancer were confirmed for 10 loci (LGR6, MDM4, CASP8, 2q35, 2p24.1, TERT-rs10069690, ESR1, TOX3, 19p13.1, RALY), and we identified associations with TN breast cancer for 15 additional breast cancer loci (P < 0.05: PEX14, 2q24.1, 2q31.1, ADAM29, EBF1, TCF7L2, 11q13.1, 11q24.3, 12p13.1, PTHLH, NTN4, 12q24, BRCA2, RAD51L1-rs2588809, MKL1). Further, two SNPs independent of previously reported signals in ESR1 [rs12525163 odds ratio (OR) = 1.15, P = 4.9 × 10(-) (4)] and 19p13.1 (rs1864112 OR = 0.84, P = 1.8 × 10(-) (9)) were associated with TN breast cancer. A polygenic risk score (PRS) for TN breast cancer based on known breast cancer risk variants showed a 4-fold difference in risk between the highest and lowest PRS quintiles (OR = 4.03, 95% confidence interval 3.46-4.70, P = 4.8 × 10(-) (69)). This translates to an absolute risk for TN breast cancer ranging from 0.8% to 3.4%, suggesting that genetic variation may be used for TN breast cancer risk prediction.

Autosomal ring chromosomes are rare abnormalities that are inherently unstable. Children with ring chromosome 6 have a wide range of intellectual functioning and congenital anomalies. Cardiac lesions are rarely reported with this chromosome abnormality. We report on a 11-year-old boy with mosaic ring chromosome 6 and a dilated aortic root.

Dyskeratosis congenita (DC) is a rare inherited form of bone marrow failure (BMF) caused by mutations in telomere maintaining genes including TERC and TERT. Here we studied the prevalence of TERC and TERT gene mutations and of telomere shortening in an unselected population of patients with BMF at our medical center and in a selected group of patients referred from outside institutions. Less than 5% of patients with BMF had pathogenic mutations in TERC or TERT. In patients with BMF, pathogenic TERC or TERT gene mutations were invariably associated with marked telomere shortening (≪ 1st percentile) in peripheral blood mononuclear cells (PBMCs). In asymptomatic family members, however, telomere length was not a reliable predictor for the presence or absence of a TERC or TERT gene mutation. Telomere shortening was not pathognomonic of DC, as approximately 30% of patients with BMF due to other causes had PBMC telomere lengths at the 1st percentile or lower. We conclude that in the setting of BMF, measurement of telomere length is a sensitive but nonspecific screening method for DC. In the absence of BMF, telomere length measurements should be interpreted with caution.

Breast cancer in young women is relatively rare compared to breast cancer occurring in older women. Younger women diagnosed with breast cancer also tend to have a more aggressive biology and consequently a poorer prognosis than older women. In addition, they face unique challenges such as diminished fertility from premature ovarian failure, extended survivorship periods and its attendant problems, and the psychosocial impact of diagnosis, while still raising families. It is therefore imperative to recognize the unique issues that younger women face, and plan management in a multidisciplinary fashion to optimize clinical outcomes. This paper discusses the challenges of breast cancer management for young women, as well as specific issues to consider in diagnosis, treatment, and follow-up of such patients.

Pleuropulmonary blastoma (PPB) is the most frequent pediatric lung tumor and often the first indication of a pleiotropic cancer predisposition, DICER1 syndrome, comprising a range of other individually rare, benign and malignant tumors of childhood and early adulthood. The genetics of DICER1-associated tumorigenesis are unusual in that tumors typically bear neomorphic missense mutations at one of five specific “hotspot” codons within the RNase IIIb domain of DICER 1, combined with complete loss of function (LOF) in the other allele. We analyzed a cohort of 124 PPB children for predisposing DICER1 mutations and sought correlations with clinical phenotypes. Over 70% have inherited or de novo germline LOF mutations, most of which truncate the DICER1 open reading frame. We identified a minority of patients who have no germline mutation, but are instead mosaic for predisposing DICER1 mutations. Mosaicism for RNase IIIb domain hotspot mutations defines a special category of DICER1 syndrome patients, clinically distinguished from those with germline or mosaic LOF mutations by earlier onsets and numerous discrete foci of neoplastic disease involving multiple syndromic organ sites. A final category of patients lack predisposing germline or mosaic mutations and have disease limited to a single PPB tumor bearing tumor-specific RNase IIIb and LOF mutations. We propose that acquisition of a neomorphic RNase IIIb domain mutation is the rate limiting event in DICER1-associated tumorigenesis, and that distinct clinical phenotypes associated with mutational categories reflect the temporal order in which LOF and RNase IIIb domain mutations are acquired during development.

Family history data are critical in the study of hereditary cancer syndromes and the identification of cancer modifier genes.The purpose of this study was to analyze the process for collecting and verifying reported cancer family histories and identify reporting inaccuracies among a series of women with endometrial cancer.Detailed family histories were obtained from 80 women enrolled in a research study. Medical records were collected to verify cancer reporting.Participants reported 289 cancers among themselves and 2925 first-, second-, and third-degree relatives. There was a significant relationship between the number of telephone contacts made with each participant and the fraction of records retrieved from hospitals (chi(2) = 23.68, d.f. = 7, P = 0.001). Medical records were retrieved for 102 of 289 (35%) reported cancers and 10 additional cancers, not initially reported by participants. Medical records were more likely to be retrieved if the relative with cancer was living, closely related to the study participant, and the cancer type was known. The success in retrieving medical records declined with increasing record age (chi(2) = 35.07, d.f. = 5, P0.001). Thirty-two of the 112 (28.6%) verified cancers were identified to be inaccurately reported, with a significantly higher number of inaccurate reports among second- and third-degree relatives than first-degree relatives (P = 0.02). Two participants, who did not accurately report their cancer family history, had an increase in their family-based risk assessment after medical record collection.Additional studies to improve record collection efficiency and identify cancer reporting accuracy are needed among general research populations.

Todora HMS, Skinner CS, Gidday L, Ivanovich JL, Rawl S and Whelan AJ. Perceptions of geneticrisk assessment and education among first-degree relatives of colorectal cancer patients andimplications for physicians. Family Practice2001; 18: 367–372.Background. Genetic risk assessment and education is a clinical service that provides anopportunity for individuals with a strong family history of cancer to understand their risk better,identify a screening regimen and discuss benefits and limitations of genetic testing. Objectives. The aim of this study was to assess knowledge of and attitudes to genetic riskassessment and education among first-degree relatives of patients with colorectal cancer.Methods. We conducted focus groups among first-degree relatives of patients with colorectalcancer to assess perceptions of genetic risk assessment and education. In the groups, we elicitedreactions using two definitions of genetic risk assessment and education—one brief and onemore detailed—that might be used by a health practitioner during the referral process. Results. Findings revealed a number of misconceptions and concerns including: (i) what isrequired to prepare for a session and a lack of desire to collect a family history; (ii) what isinvolved in a session (including assuming that genetic testing is always included in a session); (iii) distrust over accuracy and possible subjectivity of information provided; and (iv) fear of theeffect that participation in a session might have on insurance status. Conclusions. The findings suggest that health practitioners should educate individuals aboutgenetic risk assessment and education during the initial referral process. Further studies shouldexplore how best to do this.Keywords. Colorectal cancer, education, genetics, risk communication.

Recent genetic research has isolated the primary genetic defect underlying many of the hereditary colorectal cancer syndromes. Obtaining a detailed family history is the first step in identifying individuals at increased risk of developing colorectal cancer. Once identified, individuals and their families may benefit from earlier, more intensified surveillance, prophylactic surgery, cancer risk assessment and education, and genetic testing. Clinicians, especially those with many patients with colorectal cancer in their practice, must be able to address the complex issues associated with the familial and hereditary colorectal cancer syndromes. A well-integrated partnership among colorectal surgeons, gastroenterologists, oncologists, and medical geneticists is necessary to address these complex issues and provide comprehensive medical care.

BACKGROUND: Missense germ-line mutations in the RET protooncogene are associated with multiple endocrine neoplasia type 2A (MEN 2A). Detection of these mutant alleles in kindred members predicts disease inheritance and provides the basis for preventative thyroidectomy. METHODS: A polymerase chain reaction (PCR)-based genetic test for the 19 known RET mutations was designed to study 132 members of 7 kindreds with MEN 2A. Haplotypes also were constructed using genetic markers flanking the MEN 2A locus. Plasma calcitonin (CT) concentrations were determined before and after provocative testing. RESULTS: Direct DNA testing and haplotype analysis showed that 21 of 58 kindred members at risk for disease had inherited a mutation in the RET protooncogene associated with MEN 2A. Plasma CT concentrations were elevated in 9 of the 21 family members, but were normal in 12. After genetic counseling, 13 of the 21 kindred members (6 with normal and seven with elevated plasma CT levels), consented to immediate thyroidectomy. In each patient, the resected thyroid gland showed C-cell hyperplasia with or without medullary thyroid carcinoma. There were no metastases to regional lymph nodes, and postoperative stimulated plasma CT levels were normal. CONCLUSION: The PCR-based direct DNA test for RET mutations is accurate, rapid, and reproducible. For all 132 individuals evaluated, the results of direct DNA analysis were consistent with haplotype studies. The direct test for mutations in the RET protooncogene is the preferred method for screening MEN 2A kindreds. In family members who have inherited a RET mutation, total thyroidectomy is indicated, regardless of the plasma CT values.

Context The identification of patients with inherited cancer susceptibility syndromes facilitates early diagnosis, prevention, and treatment. However, in many cases of suspected cancer susceptibility, the family history is unclear and genetic testing of common cancer susceptibility genes is unrevealing. Objective To apply whole-genome sequencing to a patient without any significant family history of cancer but with suspected increased cancer susceptibility because of multiple primary tumors to identify rare or novel germline variants in cancer susceptibility genes. Design, Setting, and Participant Skin (normal) and bone marrow (leukemia) DNA were obtained from a patient with early-onset breast and ovarian cancer (negative for BRCA1 and BRCA2 mutations) and therapy-related acute myeloid leukemia (t-AML) and analyzed with the following: whole-genome sequencing using paired-end reads, single-nucleotide polymorphism (SNP) genotyping, RNA expression profiling, and spectral karyotyping. Main Outcome Measures Structural variants, copy number alterations, single-nucleotide variants, and small insertions and deletions (indels) were detected and validated using the described platforms. Results Whole-genome sequencing revealed a novel, heterozygous 3-kilobase deletion removing exons 7-9 of TP53 in the patient's normal skin DNA, which was homozygous in the leukemia DNA as a result of uniparental disomy. In addition, a total of 28 validated somatic single-nucleotide variations or indels in coding genes, 8 somatic structural variants, and 12 somatic copy number alterations were detected in the patient's leukemia genome. Conclusion Whole-genome sequencing can identify novel, cryptic variants in cancer susceptibility genes in addition to providing unbiased information on the spectrum of mutations in a cancer genome.

Abstract 580 Therapy-related acute myeloid leukemia/myelodysplasia (t-AML/t-MDS) accounts for 10–20% of all cases of AML, and its incidence is rising. Treatment options are limited and the prognosis very poor, highlighting the need for new therapies in t-AML/t-MDS. However, the genetic mutations contributing to transformation in t-AML/t-MDS are largely unknown, limiting the development of novel targeted therapeutics. Our group previously reported the sequence of the first two cancer genomes, both in patients with de novo AML (Nature 456:66, 2008; NEJM 361:1058, 2009). Herein, we report the sequence of the cancer genome of a patient with t-AML. The patient presented with early-onset breast, then ovarian cancer (age 96% of heterozygous SNPs were detected. Similar data were obtained for the skin sample. A total of 27 validated somatic single nucleotide variants or indels were detected in coding sequences. None of these mutations have been previously reported in de novo AML. Eight novel chromosomal translocations were identified and the breakpoints defined. One translocation, t(3;4)(q27.3;p15.32), resulted in the production of an in frame fusion transcript of DGKG (diacylglycerol kinase gamma) with BST1 (bone marrow cell stromal antigen 1). Studies are underway to characterize the effect of this fusion gene on hematopoietic cell growth and differentiation. In addition to -7 and del(5q), somatic copy number alterations on chromosome 3 and 12 were identified. There is controversy whether haploinsufficiency of genes on chromosomes 7 and 5q is sufficient to contribute to transformation, or whether further mutations lead to loss of heterozygosity of one or more genes in these regions. In the present case, careful review of the sequence and array data revealed no ‘homozygous' somatic single nucleotide variants, indels, or copy number alterations of coding genes on the remaining copy of chromosome 5 or 7. The patient's clinical presentation strongly suggested genetic cancer susceptibility. Analysis of the skin genome of this patient identified a heterozygous deletion of exons 7–9 of TP53, likely contributing to the early onset of her breast cancer; a uniparental disomy event resulted in the deletion being homozygous in the leukemia sample. Interestingly, the mutant TP53 allele is expressed, and it is predicted to produce a truncated p53 protein lacking most of its DNA binding domain. Functional studies of the mutant p53 protein are underway. Of note, based on a detailed family history and genotyping of the patient's mother, we suspect that the TP53 deletion occurred spontaneously. Ongoing whole genome sequencing studies in a large number of t-AML samples should identify novel somatic mutations and germline variants that contribute to t-AML. Disclosures: No relevant conflicts of interest to declare.

Pleuropulmonary blastoma (PPB) is a rare pediatric lung tumor that is often part of an inherited cancer syndrome. PPBs consist of mesenchymal cells that are susceptible to malignant transformation and cysts lined by epithelial cells. In a subset of patients, overgrowth of the cysts by mesenchymal cells leads to sarcoma formation. Here, we show that 11 multiplex PPB families harbor heterozygous germline mutations in DICER1, a gene encoding an endoribonuclease critical to the generation of small noncoding regulatory RNAs. Expression of DICER1 protein was undetectable in the epithelial component of PPB tumors but was retained in the malignant mesenchyme (sarcoma). We hypothesize that loss of DICER1 in the epithelium of the developing lung alters the regulation of diffusible factors that promote mesenchymal proliferation.

The genetic events responsible for the initiation and progression of AML are unknown for most patients. Although many important mutations for pathogenesis have been discovered, unbiased genomic approaches will be required to discover all relevant mutations. The development of “Next Generation” massively parallel sequencing approaches (454 and Solexa) have substantially reduced the cost of whole genome sequencing, and have allowed us to initiate a study designed to identify all potentially relevant mutations in a case of M1 AML. The first patient selected for study was a previously healthy 57-year-old Caucasian female who presented with a white blood count of 102,500 (91% blasts); the bone marrow biopsy revealed 100% blasts. Cytogenetics were normal. Tumor and skin (normal) samples were banked with informed consent, using our Washington University IRB-approved protocol that specifically permits whole genome sequencing. Resequencing of 14 genes frequently mutated in AML revealed somatic mutations in FLT3 (ITD) and NPM. Oligomer array-based comparative genomic hybridization using the 2.1 million-oligomer NimbleGen array revealed only one small (

Germline intragenic mutations in PTEN are associated with 80% of patients with Cowden syndrome (CS) and 60% of patients with Bannayan-Riley-Ruvalcaba syndrome (BRRS). The underlying genetic causes remain to be determined in a considerable proportion of classic CS and BRRS without a polymerase chain reaction (PCR)-detectable PTEN mutation. We hypothesized that gross gene deletions and mutations in the PTEN promoter might alternatively account for a subset of apparently mutation-negative patients with CS and BRRS. Using real time and multiplex PCR techniques, we identified three germline hemizygous PTEN deletions in 122 apparently mutation-negative patients with classic CS (N=95) or BRRS (N=27). Fine mapping suggested that one deletion encompassed the whole gene and the other two included exon 1 and encompassed exons 1–5 of PTEN, respectively. Two patients with the deletion were diagnosed with BRRS, and one patient with the deletion was diagnosed with BRRS/CS overlap (features of both). Thus 3 (11%) of 27 patients with BRRS or BRRS/CS-overlap had PTEN deletions. Analysis of the PTEN promoter revealed nine cases (7.4%) harboring heterozygous germline mutations. All nine had classic CS, representing almost 10% of all subjects with CS. Eight had breast cancers and/or benign breast tumors but, otherwise, oligo-organ involvement. PTEN protein analysis, from one deletion-positive and five PTEN-promoter-mutation–positive samples, revealed a 50% reduction in protein and multiple bands of immunoreactive protein, respectively. In contrast, control samples showed only the expected band. Further, an elevated level of phosphorylated Akt was detected in the five promoter-mutation–positive samples, compared with controls, indicating an absence of or marked reduction in functional PTEN. These data suggest that patients with BRRS and CS without PCR-detected intragenic PTEN mutations be offered clinical deletion analysis and promoter-mutation analysis, respectively.