Variants In Cohort Research Articles

Abstract P5-14-03: Clonal hematopoiesis of indeterminate potential after (neo)adjuvant chemotherapy versus endocrine therapy for early breast cancer: the CIRCE-eBC prospective cohort study

Abstract Clonal hematopoiesis of indeterminate potential after (neo)adjuvant chemotherapy versus endocrine therapy for early breast cancer: the CIRCE-eBC prospective cohort study Background: Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related condition associated with higher risk of hematologic malignancies, cardiovascular disease, and all-cause mortality. Patients (pts) with early breast cancer (eBC) receiving chemotherapy (CT) have increased risk of treatment-related myeloid neoplasms (tMN); the benefit of CT in eBC pts is often limited. Little is known about the prevalence and dynamics of CHIP in eBC pts. Methods: We prospectively identified two cohorts of pts with eBC: cohort A – pts receiving (neo)adjuvant CT with or without adjuvant endocrine therapy (ET); cohort B – pts receiving ET only. Blood was collected prior to initiation of treatment (T1) and after either (neo)adjuvant CT or 6-18 months of adjuvant ET (T2). We performed targeted sequencing of cryopreserved peripheral blood mononuclear cell (PBMC)-derived genomic DNA and defined CHIP as the presence of ≥1 pathogenic somatic mutation at variant allele fraction (VAF) ≥0.02. In additional analyses we used VAF≥0.005. Results: We enrolled 118 and 116 pts in cohorts A and B, respectively. Pts in cohort A were younger (median age 51 vs 57, p< 0.001), less frequently Caucasian (83.9 vs 96.6%; p=0.005) and former/current smokers (28.0 vs 43.1%, p=0.038). All pts in cohort B had hormone receptor-positive (HR+) eBC; in cohort A 50% of pts had HR+/HER2-, 16% had HR+/HER2+, 8.5% had HR-/HER2+ and 25.4% had HR-/HER2- eBC (p< 0.001). Pts in cohort A had higher stage (stage II-III 68.7 vs 27.6%; p< 0.001) and grade (grade 3 65.3 vs 15.5%; p< 0.001) tumors. Genetic testing was more frequently performed in pts receiving CT (88.1 vs 68.1%, p< 0.001), though the rate of germline pathogenic variants was similar (13.5 vs 17.7%, p=0.079). In cohort A, 38% received anthracyclines, 7% platinum and 57% anthracycline/platinum-sparing CT. Median time between T1 and T2 was 189.5 (150,406) and 280 (147, 425) days in cohort A and B (p< 0.001). The prevalence of CHIP, defined by mutations at VAF ≥ 0.02, was similar at T1 in cohort A (14.4%) vs B (18.1%) (p=0.556). Number of pts with new CHIP variants at T2 was also similar (A 3.4% vs B 6.0%) (p=0.373). After adjusting for age and stage, odds ratio (OR) of developing new CHIP variants in cohort B vs A was 1.28 (95% CI 0.32 – 5.68, p=0.733). Age correlated with baseline prevalence of CHIP (p< 0.001). Most frequent new CHIP variants at T2 in cohort A were DNMT3A (3), PPM1D (1), NF1 (1). To investigate whether pts receiving CT were more likely to have emergence of small hematopoietic clones, we assessed pathogenic variants present at VAF ≥0.005. These were detected at T1 in 55 (46.6%) and 61 (52.6%) pts in cohort A and B, respectively. Few pts without pathogenic variants at T1 developed them at T2 (3 pts in cohort A and 4 in cohort B). 21 pts (27 variants) in cohort A and 11 pts (12 variants) in cohort B had new variants at T2. Pts with new variants vs not (32 vs 202 pts) had similar characteristics, excepting age (median 60.5 vs 54.0, p=0.011). After correcting for age and stage, OR of developing new pathogenic variants given ET vs CT was 0.25 (95% CI 0.10-0.62, p=0.003). Most frequent newly detected variants were in DNMT3A (14), PPM1D (5), TET2 (4) and TP53 (2) in cohort A; DNMT3A (3), TET2 (3) and ZNF318 (2) in cohort B. Conclusions: In the CIRCE-eBC study, CT administration did not lead to emergence of CHIP over a 6-9 month period vs ET alone. This finding is reassuring in the setting of long life-expectancy for eBC pts and the association of CHIP with significant morbidity and mortality. However, consistent with known risk of development of MN, CT was associated with emergence of low frequency pathogenic variants in PPM1D and TP53, which have been associated with elevated risk of tMN. The evolution and prognostic role of these small clones is unclear and warrants additional investigation. Citation Format: Stefania Morganti, Qingchun Jin, Katheryn Santos, Christopher Gibson, Ashka Patel, Alex Wilson, Margaret Merrill, Julie Vincuilla, Samantha Stokes, Marla Lipsyc-Sharf, Tonia Parker, Tari King, Elizabeth A. Mittendorf, Giuseppe Curigliano, Melissa E. Hughes, Nabihah Tayob, Nancy U. Lin, Peter Miller, Sara Tolaney, Judy Garber, Heather A. Parsons. Clonal hematopoiesis of indeterminate potential after (neo)adjuvant chemotherapy versus endocrine therapy for early breast cancer: the CIRCE-eBC prospective cohort study [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-14-03.

Abstract 14506: Re-Evaluating Clinically Relevant Genes in Conotruncal Cardiac Defects by Burden Analyses of Rare and Ultra-Rare Protein-Altering Variants

Conotruncal cardiac defects (CTD) is a group of congenital heart diseases (CHD) involving malformation of outflow tract, with an estimated prevalence of 11.6 per 10,000 births. Currently, a robust consensus on causative genes for nonsyndromic CTD remains to be elucidated. To prioritize clinically relevant genes in whole exome sequencing (WES), we performed gene burden analysis on rare (gnomAD exome allele frequency < 0.01%) protein-altering variants in a cohort of nonsyndromic CTD (n = 245) comparing with ethnicity and location matched controls (n = 853); and expanded to a combined analysis of damaging ultra-rare (CADD ≥ 20 and absent in gnomAD exome) variants involving four CTD cohorts (n = 1451; 391 Chinese and 1060 Europeans) and ethnicity matched gnomAD exome singletons as controls. Gene burden analysis on variants identified within a high-confidence list of 132 CHD genes showed significant (Bonferroni corrected p-value < 0.05) excess of rare protein-altering variants in two well-established genes ( GATA6 , NOTCH1 ) and four potentially relevant genes for CTD ( ANKRD11 , DOCK6 , NPHP4 , STRA6 ). Furthermore, burden analysis of ultra-rare variants in the combined cohorts identified three genes robustly (Bonferroni corrected p-value < 0.05) associated with CTD ( FLT4 , NOTCH1 , TBX1 ). Predominantly more FLT4 loss-of-function variants were reported in Europeans than in Chinese, while GATA6 was the only gene with robust burden in Chinese but was not identified in Europeans, suggesting potential differences in the genetic landscape of CTD disease etiology among different ethnicities. Our results provided evidence of aggregate variant excess for nonsyndromic CTD in case-control comparisons and shortlisted significant genes with potential clinical relevance for further systematic curation, to guide appropriate genetic diagnosis for CTD with the application of WES.

Clinical Implications of Pathogenic Germline Variants in Small Intestine Neuroendocrine Tumors (SI-NETs).

An inherited basis for presumed sporadic neuroendocrine tumor (NET) has been suggested by evidence of familial clustering of NET and a higher incidence of second malignancies in patients and families with NET. To further investigate a potential heritable basis for sporadic neuroendocrine tumors, we performed multigene platform germline analysis to determine the frequency of hereditary susceptibility gene variants in a cohort of patients with sporadic small intestine NET (SI-NET). We performed a multigene platform germline analysis with Invitae's 83-gene, next-generation sequencing panel using DNA from 88 individuals with SI-NET from a clinically annotated database of patients with NET evaluated at Dana-Farber Cancer Institute (DFCI) who are considered high risk for inherited variants. Additionally, we evaluated the prevalence of pathogenic variants in an unselected cohort of patients with SI-NET who underwent testing with Invitae. Of the 88 patients in the DFCI cohort, a pathogenic germline variant was identified in eight (9%) patients. In an independent cohort of 120 patients with SI-NET, a pathogenic germline variant was identified in 13 (11%) patients. Pathogenic variants were identified in more than one patient in the following genes: ATM, RAD51C, MUTYH, and BLM. Somatic testing of tumors from the DFCI cohort was suboptimal because of insufficient coverage of all targeted exons, and therefore, analysis was limited. We demonstrate a 9%-11% incidence of pathogenic germline variants in genes associated with inherited susceptibility for malignancy not previously described in association with SI-NET. The association of these germline variants with neuroendocrine carcinogenesis and risk is uncertain but warrants further characterization.

Abstract 5417: Genomic analysis of infant KMT2A-r acute lymphoblastic leukemia reveals weak association with underlying germline cancer predisposition

Abstract Introduction:KMT2A (MLL) rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is a distinct leukemia with a poor prognosis, especially when compared to childhood ALL. Previous studies on KMT2A-r leukemia have demonstrated that KMT2A rearrangement can occur in utero with a short latency after birth. Infant ALL with KMT2A-r also demonstrates a low frequency of other somatic mutations. Given that germline mutations in cancer predisposition genes are found in 5-15% of children with cancer, we hypothesized that there might be distinct germline mutations in infants with this type of leukemia that could inform about leukemogenesis and biologic behavior of this entity. Methods: We performed whole genome sequencing (WGS) and whole exome sequencing (WES) on DNA isolated from 43 peripheral blood samples at the time of remission, on 3 cohorts of infants. The cohorts were comprised of infants with KMT2A-r ALL who were known to relapse (n=14) (Cohort A), infants with KMT2A-r ALL who to date have remained in remission (n=14) (Cohort B), and infants with KMT2A germline ALL (n=15) (Cohort C). Sequencing was performed using an Illumina Hiseq 4000 or 2500 to a minimum depth of 90Gb. Alignment and variant calling were performed using the Dragon Bio-IT platform (v 3.2.8, Illumina). We then looked for variants in 347 genes associated with cancer predisposition and bone marrow failure syndromes. Variants present in remission samples at a variant allele frequency of ~50%, and rare (minor allele frequency <0.1%) in control population databases (gnomAD), were considered for analysis and interpreted using ACMG/AMP variant interpretation guidelines.Results:We found 64 germline variants in cohort A (63 variants of unknown significance (VUS) and 1 likely pathogenic (LP) variant), 39 of which are associated with cancer predisposition ( 15 autosomal dominant (AD), 11 autosomal recessive (AR) and 13 others) and 25 other variants associated with bone marrow failure (BMF). In cohort B, we found 67 germline variants (64 VUS and 3 LP), 42 of which are associated with cancer predisposition (12 AD, 14 AR, and 16 others) and 25 other variants associated with bone marrow failure (BMF). Cohort C had 67 germline variants (67 VUS), 50 of which are associated with cancer predisposition (21 AD, 15 AR, and 14 others) and 17 other variants associated with bone marrow failure (BMF).Conclusion:Overall, there were no significant differences across the 3 cohorts in terms of the number and types of variants identified. Although there were germline VUS present in cancer predisposition genes in KMT2A-r infant ALL, there were no distinct recurrent pathogenic variants seen to make a significant association with an underlying cancer predisposition syndrome. Citation Format: Azhar Saeed, Midhat Farooqi, Byunggil Yoo, Rumen Kostadinov, Emily Farrow, Neil Miller, Patrick Brown, Erin Guest. Genomic analysis of infant KMT2A-r acute lymphoblastic leukemia reveals weak association with underlying germline cancer predisposition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5417.

High prevalence of rare FBLIM1 gene variants in an Italian cohort of patients with Chronic Non-bacterial Osteomyelitis (CNO)

BackgroundFBLIM1 gene has been recently demonstrated to be involved in the pathogenesis of bone sterile inflammation. The aim of the study is to evaluate the prevalence of FBLIM1 gene variants in a cohort of 80 Italian patients with Chronic Non-bacterial Osteomyelitis (CNO).MethodsThe coding regions of FBLIM1 gene were sequenced in a cohort of 80 patients with CNO using DNA extracted from blood lymphocytes, and PCR products were sequenced. Only rare (global MAF < 2%), coding variants detected were considered. Clinical evaluation of patients with rare variants and those without was performed. Fisher’s exact test was used to compare categorical and ordinal data, and Student’s t-test was used to analyze continuous data.ResultsEighteen out of 80 patients (~ 22%) presented at least one rare coding variant in FBLIM1. Eight patients presented a variant never associated before with CNO. All patients presented classical features of CNO and no statistical difference between patients with presence of FBLMI1 variants and those without were found in terms of clinical manifestation, treatment, and outcome.ConclusionConsidering the high frequency of rare variants in our CNO cohort, our data seem to confirm a possible role of FBLIM1 in the pathogenesis of CNO suggesting that CNO is a disorder of chronic inflammation and imbalanced bone remodeling.

Frequency of heterozygous germline pathogenic variants in genes for Fanconi anemia in patients with non-BRCA1/BRCA2 breast cancer: a meta-analysis.

Germline pathogenic variants in BRCA1 (FANCD1) and BRCA2 (FANCS) do not explain all familial or sporadic cases with breast cancer. Several reports indicate a role for pathogenic variants in other genes in the Fanconi anemia/breast cancer DNA repair pathway; the strengths of these associations vary widely. Publications from 2006 through 2017 were reviewed to provide a better estimate of the role of pathogenic variants in genes in this pathway in breast cancer. We identified cohorts and case-control reports describing heterozygous pathogenic variants in Fanconi anemia genes in breast cancer cases with high risk of a germline pathogenic variant in a non-BRCA1/2 breast cancer susceptibility gene ("familial"), and cases unselected for family history ("unselected"). Meta-analysis and meta-regression were used to estimate the frequencies of pathogenic variants in cohorts and the odds ratios (OR) in case-control studies. Meta-analysis of more than 100 reports of FANCN/PALB2 in familial breast cancer cases provided an overall pathogenic variant prevalence of 1.29% and an OR of 8.45. The prevalence in unselected cohorts was 0.64%, and the OR was 4.76. Pathogenic variants in FANCJ/BRIP1 had a prevalence of 0.5% in familial cases, and an OR of 1.62; their prevalence in unselected cases was 0.39%. FANCO/RAD51C, FANCP/SLX4, FANCU/XRCC2, FANCD2, and other FA-related genes all had prevalences of ≤ 0.5% among familial cases, and even lower in unselected cases. Heterozygous pathogenic variants in FANCN/PALB2 and possibly FANCJ/BRIP1 may account for 1-2% of familial non-BRCA1/2 breast cancer cases and 0.5-1% of unselected cases. Genetic counseling and testing may be suggested for unaffected relatives.

Дефицит лизосомной кислой липазы у российских больных: молекулярная характеристика и эпидемиология

Введение. Дефицит лизосомной кислой липазы (ДЛКЛ) - континуум аутосомно-рецессивно наследуемых фенотипов, обусловленных генетическими дефектами фермента лизосомной кислой липазы (ЛКЛ), играющего ключевую роль в обмене липидов. ЛКЛ кодируется геном LIPA, наиболее распространенный патогенный вариант которого -c.894G&gt;A - является причиной заболевания в более чем половине случаев. Точная частота ДЛКЛ неизвестна, в России она предположительно составляет от 1:150 000 до 1:100 000 новорожденных. Цель: биохимический скрининг на ДЛКЛ в группе высокого риска, изучение спектра мутаций гена LIPA и оценка встречаемости заболевания в г. Москве. Методы. В исследовании участвовали 1999 пациентов из различных регионов РФ с подозрением на лизосомные болезни накопления (ЛБН). Выборку для исследования носительства частого варианта гена LIPA составили сухие пятна крови 920 живых новорожденных г. Москвы. Активность ЛКЛ измерялась флуориметрическим методом в сухих пятнах крови. Кодирующая последовательность гена LIPA изучалась путём прямого секвенирования и ПДРФ-анализа. Результаты. Тридцати четырем пациентам установлен диагноз ДЛКЛ. Выявлено 16 вариантов гена LIPA, из них 11 не описаны ранее. Десять вариантов - высоковероятно патогенные, один - неясного значения. Наиболее частой мутацией в выборке был аллель c.894G&gt;A, что характерно для большинства европейских популяций. Частота данного аллеля у 920 новорожденных Москвы составила 1:270. Исходя из этого, расчетная частота встречаемости ДЛКЛ составила 1:73 159, что превышает ориентировочную оценку для РФ. Заключение. Целесообразен скрининг на ДЛКЛ пациентов с подозрением на ЛБН. Аллельная частот варианта c.894G&gt;A среди выявленных вариантов гена LIPA сопоставима с таковой в европейских исследованиях. В отличие от этих работ у российских больных встретилось относительно много различных вариантов гена, ранее описываемых крайне редко или неописанных. Расчетная частота заболеваемости ДЛКЛ в г. Москве превышает предполагаемую для РФ. Background. Lysosomal acid lipase deficiency (LALD) is a continuum of autosomal recessive diseases caused by defects in the enzyme of lipid metabolism, lysosomal acid lipase (LAL). LAL encodes by the gene LIPA. The most common variant of LIPA c.894G&gt;A caused the disease in more than а half of cases. The true frequency of LALD is unknown. In Russia it is supposed to be 1:150000 - 1:100000 of newborns. The aim of the work is the selective biochemical screening for LALD, the study of LIPA mutation spectrum and the estimation of the LALD incidence in Moscow. Materials and methods. 1999 рatients suspected of lysosomal storage diseases (LSD) took part in the study. Dried blood spots of 920 newborns of Moscow were obtained for the estimation of c.894G&gt;A allelic frequency. LAL activity was measured by fluorometric analysis. The LIPA gene was studied by direct sequencing and RFLP-analysis. Results and discussion. In 34 cases diagnosis of LALD was confirmed. Totally, 16 different variants of LIPA were found, 11 variants were novel. Ten of the novel variants were classified as pathogenic, one was uncertain significance. The allele c.894G&gt;A was the most common LIPA variant in the cohort of patients, so as in many Europe populations. The allelic frequency of the variant in the newborns collection was estimated as 1:270 and LALD frequence was 1:73.159. Conclusion. Screening for LALD is a useful tool for diagnostics among LSD suspected patients. The allelic frequency of the variant c.894G&gt;A seems the same as in European populations. In comparison with this data, there are many rare and novel variants in the Russian cohort.

Phenotypic spectrum associated with a CRADD founder variant underlying frontotemporal predominant pachygyria in the Finnish population.

Intellectual disability (ID), megalencephaly, frontal predominant pachygyria, and seizures, previously called "thin" lissencephaly, are reported to be caused by recessive variants in CRADD. Among five families of different ethnicities identified, one homozygous missense variant, c.509G>A p.(Arg170His), was of Finnish ancestry. Here we report on the phenotypic variability associated for this potential CRADD founder variant in 22 Finnish individuals. Exome sequencing was used to identify candidate genes in Finnish patients presenting with ID. Targeted Sanger sequencing and restriction enzyme analysis were applied to screen for the c.509G>A CRADD variant in cohorts from Finland. Detailed phenotyping and genealogical studies were performed. Twenty two patients were identified with the c.509G>A p.(Arg170His) homozygous variant in CRADD. The majority of the ancestors originated from Northeastern Finland indicating a founder effect. The hallmark of the disease is frontotemporal predominant pachygyria with mild cortical thickening. All patients show ID of variable severity. Aggressive behavior was found in nearly half of the patients, EEG abnormalities in five patients and megalencephaly in three patients. This study provides detailed data about the phenotypic spectrum of patients with lissencephaly due to a CRADD variant that affects function. High inter- and intrafamilial phenotypic heterogeneity was identified in patients with pachygyria caused by the homozygous CRADD founder variant. The phenotype variability suggests that additional genetic and/or environmental factors play a role in the clinical presentation. Since frontotemporal pachygyria is the hallmark of the disease, brain imaging studies are essential to support the molecular diagnosis for individuals with ID and a CRADD variant.

Prevalence of Germline Variants in Prostate Cancer and Implications for Current Genetic Testing Guidelines

Prostate cancer is the third leading cause of cancer-related death in men in the United States. Although serious, most of these diagnoses are not terminal. Inherited risk for prostate cancer is associated with aggressive disease and poorer outcomes, indicating a critical need for increased genetic screening to identify disease-causing variants that can pinpoint individuals at increased risk for metastatic castration-resistant prostate cancer. To identify positive (pathogenic, likely pathogenic, and increased risk) germline variants in a large prostate cancer cohort and to evaluate the usefulness of current practice guidelines in recognizing individuals at increased risk for prostate cancer who would benefit from diagnostic genetic testing. Cross-sectional study of data from 3607 men with a personal history of prostate cancer who underwent germline genetic testing between 2013 and 2018 and were unselected for family history, stage of disease, or age at diagnosis. Referral-based testing was performed at a Clinical Laboratory Improvement Amendments/College of American Pathologists-certified diagnostic laboratory. All analysis took place between February 2017 and August 2018. The frequency and distribution of positive germline variants, and the percentage of individuals with prostate cancer who met National Comprehensive Cancer Network (NCCN) guidelines for germline genetic testing. Of 3607 men (mean [SD] age at testing, 67 [9.51] years; mean age at diagnosis, 60 [9.05] years) with a personal diagnosis of prostate cancer who were referred for genetic testing, 620 (17.2%) had positive germline variants, of which only 30.7% were variants in BRCA1/2. Positive variants in HOXB13, a gene associated only with prostate cancer risk, were identified in 30 patients (4.5%). DNA mismatch repair variants with substantial known therapeutic implications were detected in 1.74% of variants in the total population tested. Examination of self-reported family histories indicated that 229 individuals (37%) with positive variants in this cohort would not have been approved for genetic testing using the NCCN genetic/familial breast and ovarian guidelines for patients with prostate cancer. Current NCCN guidelines and Gleason scores cannot reliably stratify patients with prostate cancer for the presence or absence of pathogenic germline variants. Most positive genetic test results identified in this study have important management implications for patients and their families, which underscores the need to revisit current guidelines.

Exome Sequencing–Based Screening for BRCA1/2 Expected Pathogenic Variants Among Adult Biobank Participants

Detection of disease-associated variants in the BRCA1 and BRCA2 (BRCA1/2) genes allows for cancer prevention and early diagnosis in high-risk individuals. To identify pathogenic and likely pathogenic (P/LP) BRCA1/2 variants in an unselected research cohort, and to characterize the features associated with P/LP variants. This is a cross-sectional study of adult volunteers (n = 50 726) who underwent exome sequencing at a single health care system (Geisinger Health System, Danville, Pennsylvania) from January 1, 2014, to March 1, 2016. Participants are part of the DiscovEHR cohort and were identified through the Geisinger MyCode Community Health Initiative. They consented to a research protocol that included sequencing and return of actionable test results. Clinical data from electronic health records and clinical visits were correlated with variants. Comparisons were made between those with (cases) and those without (controls) P/LP variants in BRCA1/2. Prevalence of P/LP BRCA1/2 variants in cohort, proportion of variant carriers not previously ascertained through clinical testing, and personal and family history of relevant cancers among BRCA1/2 variant carriers and noncarriers. Of the 50 726 health system patients who underwent exome sequencing, 50 459 (99.5%) had no expected pathogenic BRCA1/2 variants and 267 (0.5%) were BRCA1/2 carriers. Of the 267 cases (148 [55.4%] were women and 119 [44.6%] were men with a mean [range] age of 58.9 [23-90] years), 183 (68.5%) received clinically confirmed results in their electronic health record. Among the 267 participants with P/LP BRCA1/2 variants, 219 (82.0%) had no prior clinical testing, 95 (35.6%) had BRCA1 variants, and 172 (64.4%) had BRCA2 variants. Syndromic cancer diagnoses were present in 11 (47.8%) of the 23 deceased BRCA1/2 carriers and in 56 (20.9%) of all 267 BRCA1/2 carriers. Among women, 31 (20.9%) of 148 variant carriers had a personal history of breast cancer, compared with 1554 (5.2%) of 29 880 noncarriers (odds ratio [OR], 5.95; 95% CI, 3.88-9.13; P < .001). Ovarian cancer history was present in 15 (10.1%) of 148 variant carriers and in 195 (0.6%) of 29 880 variant noncarriers (OR, 18.30; 95% CI, 10.48-31.4; P < .001). Among 89 BRCA1/2 carriers without prior testing but with comprehensive personal and family history data, 44 (49.4%) did not meet published guidelines for clinical testing. This study found that compared with previous clinical care, exome sequencing-based screening identified 5 times as many individuals with P/LP BRCA1/2 variants. These findings suggest that genomic screening may identify BRCA1/2-associated cancer risk that might otherwise remain undetected within health care systems and may provide opportunities to reduce morbidity and mortality in patients.

New rare genetic variants of LMF1 gene identified in severe hypertriglyceridemia

The LMF1 (lipase maturation factor 1) gene encodes a protein involved in lipoprotein lipase and hepatic lipase maturation. Homozygous mutations in LMF1 leading to severe hypertriglyceridemia (SHTG) are rare in the literature. A few additional rare LMF1 variants have been described with poor functional studies. The aim of this study was to assess the frequency of LMF1 variants in a cohort of 385 patients with SHTG, without homozygous or compound heterozygous deleterious mutations identified in lipoprotein lipase (LPL), apolipoprotein A5 (APOA5), apolipoprotein C2 (APOC2), glycosylphosphatidylinositol-anchored high-density lipoprotein binding protein 1 (GPIHBP1) genes, and to determine their functionality. LMF1 coding variants were screened using denaturing high-performance liquid chromatography followed by direct sequencing. In silico studies of LMF1 variants were performed, followed by invitro functional studies using human embryonic kidney 293T (HEK-293T) cells cotransfected with vectors encoding human LPL and LMF1 cDNA. LPL activity was measured in cell culture medium after heparin addition using human VLDL-TG as substrate. Nineteen nonsynonymous coding LMF1 variants were identified in 65 patients; 10 variants were newly described in SHTG. Invitro, p.Gly172Arg, p.Arg354Trp, p.Arg364Gln, and p.Arg537Trp LMF1 variants decreased LPL activity, and the p.Trp464Ter variant completely abolished LPL activity. We identified a young girl heterozygote for the p.Trp464Ter variant and a homozygote carrier of the p.Gly172Arg variant with a near 50% decreased LPL activity invitro and invivo. The study confirms the rarity of LMF1 variants in a large cohort of patients with SHTG. LMF1 variants are likely to be involved in multifactorial hyperchylomicronemia. Partial LMF1 defects could be associated with intermittent phenotype as described for p.Gly172Arg homozygous and p.Trp464Ter heterozygous carriers.

The prevalence of APOL1 gene variants in a cohort of renal disease patients in Western Saudi Arabia.

Two variants for APOL1; the gastrointestinal (G1) variant (S342G and 1384M substitutions) and the G2 variant (N388 and Y389 deletions) have been previously described to be associated with renal disease. The prevalence of APOL1 variants in Saudi Arabia is unknown. We aimed to determine the prevalence of APOL1 variants in a cohort of patients with renal disease in Saudi Arabia. Patients with renal disease followed up at King Abdulaziz University Hospital were approached consecutively at the out patient clinic, and unaffected controls were approached at the blood donation area. Clinical and laboratory data were collected from electronic medical records. Laboratory variables in controls were obtained on enrollment. This is a cross-sectional, cohort study. One hundred and one patients with a mean age of 54.5 (±19) years, and 119 unaffected controls with a mean age of 31.9 (±7.89) years, were enrolled. Seventy-four patients (68.5%) had hypertension and 62 (57.4%) had diabetes. The mean estimated glomerular filtration rate was 22.47 (± 27.6) mL/min. Two patients were heterozygous for G1 allele. Among the control group, two were heterozygous for G1 allele, and three were heterozygous for G2. All five controls had no evidence of renal disease and no family history of renal disease. The prevalence of APOL1 genetic risk variants in the study cohort was very low. Larger studies are needed to determine the prevalence among renal disease patients in Saudi Arabia.

Measuring shared variants in cohorts of discordant siblings with applications to autism

We develop a method of analysis [affected to discordant sibling pairs (A2DS)] that tests if shared variants contribute to a disorder. Using a standard measure of genetic relation, test individuals are compared with a cohort of discordant sibling pairs (CDS) to derive a comparative similarity score. We ask if a test individual is more similar to an unrelated affected than to the unrelated unaffected sibling from the CDS and then, sum over such individuals and pairs. Statistical significance is judged by randomly permuting the affected status in the CDS. In the analysis of published genotype data from the Simons Simplex Collection (SSC) and the Autism Genetic Resource Exchange (AGRE) cohorts of children with autism spectrum disorder (ASD), we find strong statistical significance that the affected are more similar to the affected than to the unaffected of the CDS (P value ∼ 0.00001). Fathers in multiplex families have marginally greater similarity (P value = 0.02) to unrelated affected individuals. These results do not depend on ethnic matching or gender.

S08 * ESBRA-NIAAA JOINT SYMPOSIUM ALCOHOLIC LIVER DISEASE: FROM PATHOGENESIS TO TREATMENT * S08.1 * INCREASING BURDEN OF ALCOHOLIC LIVER DISEASE 2011

S08 * ESBRA-NIAAA JOINT SYMPOSIUM ALCOHOLIC LIVER DISEASE: FROM PATHOGENESIS TO TREATMENT * S08.1 * INCREASING BURDEN OF ALCOHOLIC LIVER DISEASE 2011

Variants of CCR5, which are permissive for HIV-1 infection, show distinct functional responses to CCL3, CCL4 and CCL5

CCR5 is one of the primary coreceptors for Env-mediated fusion between cells and human immunodeficiency virus type 1 (HIV-1). Analyses of CCR5 variants in cohorts of HIV-1 high-risk individuals led to the identification of multiple single amino-acid substitutions, which may have functional consequences. This study focused on eight naturally occurring allelic variants located between amino-acid residues 60 and 334 of CCR5. All studied allelic variants were highly expressed on the cell surface of HEK-293 cells and permissive for HIV-1 infection. Variant G301V showed 3.5-fold increase in 50% effective concentration (EC(50)) for CCL4 (MIP 1beta) in a competitive binding assay. There was also a significant reduction in CCL5 (RANTES) EC(50) for the R223Q, A335V and Y339F variants. The most unexpected functional abnormality was exhibited by the R60S variant that exhibited a loss of ligand-induced desensitization in chemotaxis assays, but showed normal CCL4 and CCL5 binding avidity. This mutation is located in the first intracellular loop, a domain that has not previously been shown to be involved in receptor desensitization. In conclusion, our results support earlier studies showing that these naturally occurring point mutations do not limit HIV-1 infection, and indicated that single amino-acid changes can have unexpected functional consequences.