Sari Lieberman

Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families

BackgroundIdentification of genes responsible for medically important traits is a major challenge in human genetics. Due to the genetic heterogeneity of hearing loss, targeted DNA capture and massively parallel sequencing are ideal tools to address this challenge. Our subjects for genome analysis are Israeli Jewish and Palestinian Arab families with hearing loss that varies in mode of inheritance and severity.ResultsA custom 1.46 MB design of cRNA oligonucleotides was constructed containing 246 genes responsible for either human or mouse deafness. Paired-end libraries were prepared from 11 probands and bar-coded multiplexed samples were sequenced to high depth of coverage. Rare single base pair and indel variants were identified by filtering sequence reads against polymorphisms in dbSNP132 and the 1000 Genomes Project. We identified deleterious mutations in CDH23, MYO15A, TECTA, TMC1, and WFS1. Critical mutations of the probands co-segregated with hearing loss. Screening of additional families in a relevant population was performed. TMC1 p.S647P proved to be a founder allele, contributing to 34% of genetic hearing loss in the Moroccan Jewish population.ConclusionsCritical mutations were identified in 6 of the 11 original probands and their families, leading to the identification of causative alleles in 20 additional probands and their families. The integration of genomic analysis into early clinical diagnosis of hearing loss will enable prediction of related phenotypes and enhance rehabilitation. Characterization of the proteins encoded by these genes will enable an understanding of the biological mechanisms involved in hearing loss.

Mutations in FKBP10, which result in Bruck syndrome and recessive forms of osteogenesis imperfecta, inhibit the hydroxylation of telopeptide lysines in bone collagen

Although biallelic mutations in non-collagen genes account for <10% of individuals with osteogenesis imperfecta, the characterization of these genes has identified new pathways and potential interventions that could benefit even those with mutations in type I collagen genes. We identified mutations in FKBP10, which encodes the 65 kDa prolyl cis-trans isomerase, FKBP65, in 38 members of 21 families with OI. These include 10 families from the Samoan Islands who share a founder mutation. Of the mutations, three are missense; the remainder either introduce premature termination codons or create frameshifts both of which result in mRNA instability. In four families missense mutations result in loss of most of the protein. The clinical effects of these mutations are short stature, a high incidence of joint contractures at birth and progressive scoliosis and fractures, but there is remarkable variability in phenotype even within families. The loss of the activity of FKBP65 has several effects: type I procollagen secretion is slightly delayed, the stabilization of the intact trimer is incomplete and there is diminished hydroxylation of the telopeptide lysyl residues involved in intermolecular cross-link formation in bone. The phenotype overlaps with that seen with mutations in PLOD2 (Bruck syndrome II), which encodes LH2, the enzyme that hydroxylates the telopeptide lysyl residues. These findings define a set of genes, FKBP10, PLOD2 and SERPINH1, that act during procollagen maturation to contribute to molecular stability and post-translational modification of type I procollagen, without which bone mass and quality are abnormal and fractures and contractures result.

Population screening for BRCA1/BRCA2 founder mutations in Ashkenazi Jews: proactive recruitment compared with self-referral.

Purpose:Population screening of three common BRCA1/BRCA2 mutations in Ashkenazi Jews (AJ) apparently fulfills screening criteria. We compared streamlined BRCA screening via self-referral with proactive recruitment in medical settings.Methods:Unaffected AJ, age ≥25 years without known familial mutations, were either self-referred or recruiter-enrolled. Before testing, participants received written information and self-reported family history (FH). After testing, both non-carriers with significant FH and carriers received in-person genetic counseling. Psychosocial questionnaires were self-administered 1 week and 6 months after enrollment.Results:Of 1,771 participants, 58% were recruiter-enrolled and 42% were self-referred. Screening uptake was 67%. Recruited enrollees were older (mean age 54 vs. 48, P < 0.001) and had less suggestive FH (23 vs. 33%, P < 0.001). Of 32 (1.8%) carriers identified, 40% had no significant FH. Post-test counseling compliance was 100% for carriers and 89% for non-carrier women with FH. All groups expressed high satisfaction (>90%). At 6 months, carriers had significantly increased distress and anxiety, greater knowledge, and similar satisfaction; 90% of participants would recommend general AJ BRCA screening.Conclusion:Streamlined BRCA screening results in high uptake, very high satisfaction, and no excess psychosocial harm. Proactive recruitment captured older women less selected for FH. Further research is necessary to target younger women and assess other populations.Genet Med advance online publication 08 December 2016

Population screening for BRCA1/BRCA2 mutations: lessons from qualitative analysis of the screening experience

Purpose:Population screening for BRCA1/BRCA2. mutations is being considered for Ashkenazi Jews (AJ) because 2.5% carry recurrent deleterious mutations and effective cancer prevention exists. This study aimed to provide a qualitative focus on perspectives of individuals, particularly carriers, who were tested through a screening trial. In this trial, the pretest process included only written information.Methods:Interviews were performed with 26 carriers and 10 noncarriers who participated in a BRCA population screening trial for AJ.Results:Attitudes toward screening were generally positive. The main motivator for testing was knowledge of BRCA status to enable cancer risk reduction. Knowledge of carrier status, although challenging, was thus viewed as health-empowering. The screening paradigm was sensed as increasing awareness and as overcoming access, referral, and familial barriers. Streamlining the pretest process was positively perceived as offering gradual, stepwise knowledge commensurate with test results. Participants were concerned that health systems provide the necessary conceptual and infrastructural framework and that individual autonomy be maintained.Conclusions:BRCA screening in AJ is viewed favorably, even by carriers. Stepwise acquisition of knowledge based on test results was viewed as most relevant to the screening context. Screening program development should account for safeguarding autonomy and providing requisite post-test services.Genet Med advance online publication 01 December 2016

Features of Patients With Hereditary Mixed Polyposis Syndrome Caused by Duplication of GREM1 and Implications for Screening and Surveillance

Hereditary mixed polyposis syndrome is a rare colon cancer predisposition syndrome caused by a duplication of a noncoding sequence near the gremlin 1, DAN family BMP antagonist gene (GREM1) originally described in Ashkenazi Jews. Few families with GREM1 duplications have been described, so there are many questions about detection and management. We report 4 extended families with the duplication near GREM1 previously found in Ashkenazi Jews; 3 families were identified at cancer genetic clinics in Israel and 1 family was identified in a cohort of patients with familial colorectal cancer. Their clinical features include extracolonic tumors, onset of polyps in adolescence, and rapid progression of some polyps to advanced adenomas. One family met diagnostic criteria for Lynch syndrome. Expansion of the hereditary mixed polyposis syndrome phenotype can inform surveillance strategies for carriers of GREM1 duplications.

Conflicts regarding genetic counseling for fragile X syndrome screening: a survey of clinical geneticists and genetic counselors in Israel.

Although fragile X screening has been offered in Israel since 1994, issues related to potential neurological and gynecological symptoms in carriers make counseling for fragile X different from recessive disorders. We evaluated the attitudes of clinical geneticists and genetic counselors regarding genetic counseling given to the women undergoing screening. We performed a self‐administered questionnaire including 13 study questions mailed to all clinical geneticists and genetic counselors in Israel. The questions were related to counseling for women pre‐ and post‐screening regarding themselves and the affected fetuses (including the risk for premature ovarian insufficiency; FXPOI and fragile X‐associated tremor ataxia syndrome; FXTAS). Out of a total of 80 clinical geneticists and genetic counselors, 34 responded with no additional responses on e‐mail re‐call. There was no clear consensus for 11/13 (85%) presented questions. The most striking differences in opinion were observed for issues regarding FXTAS risk in pre‐screening counseling sessions (P < 0.05). This study demonstrates that, there is no consensus on critical variables implying risk for fetus and mother and that counseling practices are dissimilar even in this small cohort of experts. We demonstrated a conflict between the detailed amount of information, which should be given prior to the test in order to allow informed decisions and the overload of information, which may cause confusion.

Prenatal Isolated Ventricular Septal Defect May Not Be Associated with Trisomy 21

The aim of this study was to examine if isolated fetal ventricular septal defect (VSD) is associated with trisomy 21. One hundred twenty six cases with prenatal VSD diagnosed by a pediatric cardiologist were reviewed. Cases with known risk factors for congenital heart disease, the presence of other major anomalies, soft signs for trisomy 21 or a positive screen test for trisomy 21 were excluded. Ninety two cases formed the study group. None of the cases in the study group had trisomy 21. The upper limit of prevalence for trisomy 21 in isolated VSD is 3%. When prenatal VSD is not associated with other major anomalies, soft markers for trisomy 21 or a positive nuchal translucency or biochemical screen, a decision whether to perform genetic amniocentesis should be individualized. The currently unknown association between isolated VSD and microdeletions and microduplications should be considered when discussing this option.

Familial communication and cascade testing among relatives of BRCA population screening participants

PurposePopulation BRCA1/BRCA2 screening identifies carriers irrespective of family history, yet this information is actionable for relatives. We examined familial communication rates and cascade testing in the screening setting and assessed sociodemographic and psychosocial predictors.MethodsParticipants in a BRCA1/BRCA2 screening study of healthy Ashkenazi Jews self-administered a family communication questionnaire. Intent to communicate was determined before genetic status was known, along with result communication (carriers and noncarriers) 6 months and 2 years after enrollment. Carriers underwent in-depth interviews and provided cascade testing information.ResultsIn total, 88% (524/595) of questionnaire responders and 97% (30/32) of carriers informed at least one relative. In multivariate analysis, family history (P = 0.005) and greater Satisfaction With Health Decision scores (P < 0.001) predicted communication of results. Among carriers’ adult first- and second-degree relatives, 71 (48%) had cascade testing, more commonly performed in first- (58%) than in second-degree relatives (26%, P = 0.0002), and in females (56%) vs. males (36%, P = 0.02). At least 11% remained uninformed.ConclusionFamilial communication rates and characteristics in a screening setting parallel those reported by Cancer Genetics clinics. Universal screening circumvents dependence on familial disclosure. However, our finding that satisfaction—a potentially modifiable factor—predicts communication, raises the hypothesis that improving the testing experience could facilitate familial communication.