Effective Genetic Counseling Research Articles

Whole-genome mate-pair sequencing of apparently balanced chromosome rearrangements reveals complex structural variations: two case studies

BackgroundApparently balanced chromosome rearrangements (ABCRs) in non-affected individuals are well-known to possess high reproductive risks such as infertility, abnormal offspring, and pregnancy loss. However, caution should be exercised in genetic counseling and reproductive intervention because cryptic unbalanced defects and genome structural variations beyond the resolution of routine cytogenetics may not be detected.Case presentationHere, we studied two familial cases of ABCRs were recruited in this study. In family 1, the couple suffered two abortions pregnancies and underwent labor induction. Single nucleotide polymorphism (SNP) array analysis of the aborted sample from the second pregnancy revealed a 10.8 Mb heterozygous deletion at 10q26.13q26.3 and a 5.5 Mb duplication at 19q13.41-q13.43. The non-affected father was identified as a carrier of three-way complex chromosomal rearrangement [t (6;10;19)(p22;q26;q13)] by karyotyping. Whole-genome mate-pair sequencing revealed a cryptic breakpoint on the derivative chromosome 19 (der19), indicating that the karyotype was a more complex structural rearrangement comprising four breakpoints. Three genes, FAM24B, CACNG8, and KIAA0556, were disrupted without causing any abnormal phenotype in the carrier. In family 2, the couple suffered from a spontaneous miscarriage. This family had an affected child with multiple congenital deformities and an unbalanced karyotype, 46,XY,der (11) t (6;11)(q13;p11.2). The female partner was identified as a balanced translocation carrier with the karyotype 46,XX,t (6;11)(q13;p11.2) dn. Further SNP array and fluorescent in situ hybridization (FISH) indicated a cryptic insertion between chromosome 6 and chromosome 11. Finally, whole-genome mate-pair sequencing revealed an extremely complex genomic structural variation, including a cryptic deletion and 12 breakpoints on chromosome 11, and 1 breakpoint on chromosome 6 .ConclusionsOur study investigated two rare cases of ABCRs and demonstrated the efficacy of whole-genome mate-pair sequencing in analyzing the genome complex structural variation. In case of ABCRs detected by conventional cytogenetic techniques, whole genome sequencing (WGS) based approaches should be considered for accurate diagnosis, effective genetic counseling, and correct reproductive intervention to avoid recurrence risks.

Genotype-Phenotype Correlation of β-Thalassemia in Malaysian Population: Toward Effective Genetic Counseling

Effective prevention of β-thalassemia (β-thal) requires strategies to detect at-risk couples. This is the first study attempting to assess the prevalence of silent β-thal carriers in the Malaysian population. Hematological and clinical parameters were evaluated in healthy blood donors and patients with β-thal trait, Hb E (HBB: c.79G>A)/β-thal and β-thal major (β-TM). β-Globin gene sequencing was carried out for 52 healthy blood donors, 48 patients with Hb E/β-thal, 34 patients with β-TM and 38 patients with β-thal trait. The prevalence of silent β-thal carrier phenotypes found in 25.0% of healthy Malaysian blood donors indicates the need for clinician’s awareness of this type in evaluating β-thal in Malaysia. Patients with β-TM present at a significantly younger age at initial diagnosis and require more blood transfusions compared to those with Hb E/β-thal. The time at which genomic DNA was extracted after blood collection, particularly from patients with β-TM and Hb E/β-thal, was found to be an important determinant of the quality of the results of the β-globin sequencing. Public education and communication campaigns are recommended as apparently healthy individuals have few or no symptoms and normal or borderline hematological parameters. β-Globin gene mutation characterization and screening for silent β-thal carriers in regions prevalent with β-thal are recommended to develop more effective genetic counseling and management of β-thal.

Trans-inclusive genetic counseling services: Recommendations from members of the transgender and non-binary community.

The term transgender is used to describe individuals whose gender identity does not align with their sex assigned at birth. The term transgender can include individuals who identify as men, as women, as both of the traditional concepts of masculine and feminine gender, or neither masculine or feminine. The latter two gender identities may also be known as non-binary or gender non-conforming identities. Transgender individuals may attend genetic counseling for a variety of reasons, but current pedigree nomenclature does not adequately represent both sex assigned at birth (which is important for determining risk for certain conditions) and gender (which is important for providing trans-inclusive care). We conducted an interpretive description (qualitative, interview based) study with individuals from the transgender community to gather insight on pedigree nomenclature and more broadly, how to provide safe and effective genetic counseling for transgender individuals. We conducted semi-structured telephone interviews with individuals who identified as transgender or gender non-binary, transcribed them verbatim, and checked them for accuracy before coding and inductively identifying themes. Among our eight participants, five identified as trans-masculine, two as trans-feminine, five as non-binary/gender non-conforming (some participants had more than one gender identity). From the interviews, we identified a single key, over-arching theme: participants' felt it is the genetic counselor's responsibility to create safety and provide clarity about the clinical importance of both sex assigned at birth and gender identity for trans patients. Two specific strategies that counselors could use to achieve this safety and clarity were discussed extensively: (a) validating gender identity and (b) using inclusive and well-defined pedigree symbols that denote both sex assigned at birth and gender identity. Our data have important practice implications in terms of the importance of validating gender identity and using respectful pedigree symbols.

Identification of a Novel Frameshift Variant of POU3F4 and Genetic Counseling of Korean Incomplete Partition Type III Subjects Based on Detailed Genotypes.

Aim: The aim of this study was to report a novel POU Class 3 Homeobox 4 (POU3F4) variant and to provide further guidance on genetic counseling for incomplete partition (IP) type III families in the Korean population by showing two new contrasting cases in terms of genotypes and inheritance. Materials and Methods: Two consecutively recruited hearing-impaired probands with seemingly nonsyndromic features and their biological mothers were included in this study. Sanger sequencing and quantitative polymerase chain reaction (PCR) assays were performed for POU3F4. Results: A novel frameshift variant of POU3F4, c.852delC (p.Ile285Serfs*3), was identified in one of the patients. This mutation is predicted to truncate the protein within the POU homeodomain, resulting in the complete loss of the last nucleus localization signal. The proband's biological mother was also shown to be a carrier of this c.852delC (p.Ile285Serfs*3) mutant allele. A de novo genomic deletion on chromosome Xq21.2 was confirmed in another subject via quantitative PCR. This subject's biological mother, however, was not a carrier of this deletion. This indicates that the large upstream deletion of POU3F4 in the second proband occurred de novo. This finding is compatible with the previously proposed tendency for a high de novo rate of large genomic deletions involving the X-linked deafness-2 (DFNX2) locus. Conclusion: This study adds a novel, probably pathogenic POU3F4 truncation variant to the literature and provides guidance toward effective genetic counseling for IP III subjects based on more frequent de novo occurrence of POU3F4 deletions than POU3F4 point variants.

Prenatal diagnosis of sex chromosome mosaicism with two marker chromosomes in three cell lines and a review of the literature.

The present study described the diagnosis of a fetus with sex chromosome mosaicism in three cell lines and two marker chromosomes. A 24‑year‑old woman underwent amniocentesis at 21weeks and 4days of gestation due to noninvasive prenatal testing identifying that the fetus had sex chromosome abnormalities. Amniotic cell culture revealed a karyotype of 45,X[13]/46,X,+mar1[6]/46,X,+mar2[9], and prenatal ultrasound was unremarkable. The woman underwent repeat amniocentesis at 23weeks and 4days of gestation for molecular detection. Single nucleotide polymorphism (SNP) microarray analysis on uncultured amniocytes revealed that the fetus had two Y chromosomes and 7.8‑Mb deletions in Yq11.222q12. The deletion regions included DAZ, RBMY and PRY genes, which could cause spermatogenesis obstacle and sterility. Interphase fluorescence insitu hybridization (FISH) using centromeric probes DXZ1/DYZ3/D18Z1 was performed on uncultured amniocytes to verify the two marker chromosomes to be Y chromosome derivatives. According to these examinations, the mar1 was identified as a derivative of the Y chromosome with a deletion in Yq11.222q12, and the mar2 was identified as a dicentric derivative of the Y chromosome. The molecular karyotype was therefore 45,X,ish(DXZ1+, DYZ3‑,D18Z1++)[5]/46,X,del(Y)(q11.222),ish(DXZ1+,DYZ3+,D18Z1++)[11]/46, X,idic(Y)(q11.222),ish(DXZ1+,DYZ3++,D18Z1++)[14]. The comprehensive use of cytogenetic, SNP array and FISH detections was advantageous for accurately identifying the karyotype, identifying the origin of the marker chromosome and preparing effective genetic counseling.

Precision Medicine: Familiarity, Perceived Health Drivers, and Genetic Testing Considerations Across Health Literacy Levels in a Diverse Sample.

A clear awareness of a patient's knowledge, values, and perspectives is an important component of effective genetic counseling. Advances in precision medicine, however, have outpaced our understanding of patient perceptions of this new approach. Patient views may differ across the three domains of precision medicine (genetics, behavioral, and environmental determinants of health), ethnic/racial groups, and health literacy levels. This study describes and compares group differences in familiarity, perceptions, and preferences for precision medicine in a diverse sample. Between 2016 and 2017, 252 participants completed a 10-15-min survey in three primary care clinics in Florida and Tennessee. The final sample was 42.5% African American/Black, 25.8% Hispanic/Latino, 25.0% White, and 6.7% other ethnicity/race. Less than a quarter of participants reported being familiar with the term "precision medicine," but were more familiar with basic genetic terms. Participants with higher health literacy reported greater familiarity with terms (p ≤ .003). African Americans/Black participants were more likely to identify ethnicity/race and discrimination as influencing their health (p ≤ .004). When deciding to get a genetic test, individuals across ethnic/racial groups shared similar considerations. Those with higher health literacy, however, gave significantly greater importance to provider trust (p ≤ .008). Given the recent emergence of precision medicine, at present there may be limited differences in patient perceptions across ethnic/racial groups. Culturally sensitive efforts, tailored to health literacy level, may aid equitable precision medicine uptake.

A Comprehensive Program Enabling Effective Delivery of Regional Genetic Counseling

The aim of this study was to demonstrate the utility of a comprehensive program involving management-based evidence, telemedicine, and patient navigation to provide genetic counseling services for patients with ovarian and breast cancer across a geographically large health care system. We identified all patients with newly diagnosed ovarian and breast cancer in our health care system from January 2013 to December 2015 through the cancer registry. Referral characteristics and testing outcomes were recorded for each year and compared using the χ or Fisher exact test. Because the implementation of this program, the number of new ovarian cancer cases remained constant (109-112 cases/year) but patients referred for genetic counseling increased annually from 37% to 43% to 96% (P < 0.05). The percentage of ovarian cancer patients who underwent genetic testing increased annually from 24% to 27% to 53% (P < 0.05). The number of new breast cancer patients was constant (1543-1638 cases/year). The percentage of patients with triple negative breast cancer referred for genetic counseling rose from 69% in 2013 to 91% in 2015; the percentage of patients who underwent testing increased annually from 59% to 86% (P < 0.05). Of women with breast cancer diagnosed at less than 45 years of age, 78% to 85% were referred for genetic counseling across this period; the percentage of patients who underwent testing increased annually from 66% to 82% (P < 0.05). Patient navigation was initiated and was available to all patients in the system during this period. Telemedicine consults were performed in 118 breast/ovarian patients (6%) during this period. A comprehensive program may improve access to effective genetic counseling services in patients with ovarian and breast cancer despite geographic barriers.

Characteristics of genetic diseases in consanguineous populations in the genomic era: Lessons from Arab communities in North Israel.

The health outcome of consanguineous/endogamous unions is an increased risk of autosomal recessive disorders in their progeny. This manuscript is focused on consanguineous/endogamous populations living in North Israel. Molecular tools show that spouses' relatedness and hence their risks for congenital diseases among offspring are often greater than the risk calculated on the basis of reported pedigrees. Revealing founder mutations allow for effective genetic counseling, but also induce genetic screening of the whole community in case the mutations are found to be frequent. More complex genetic mechanisms, such as co-inheritance of more than one condition, allelic and even locus heterogeneity, have been identified. These mechanisms make genetic counseling more challenging but with the advancement of molecular techniques, diseases can be better deciphered. Yet, the presence of multiple mutations responsible for genetic diseases in isolated populations, and occasionally locus heterogeneity of diseases, is an unexpected phenomenon that still needs mechanistic clarification. It seems probably that addressing genetic counseling challenges and estimations of risks for genetic morbidity in consanguineous/endogamous couples will be achieved by introducing high-throughput genetic technologies into daily practice. The genomic era has expanded dramatically the translation of research products to genetic counseling tools, and this tendency is expected to yield a stronger impact in a near future.

A CDH3 Mutation is Segregated in an Iranian Family with Congenital Hypotrichosis and Juvenile Macular Dystrophy

Backgrounds Hypotrichosis with juvenile macular dystrophy (HJMD) is a rare genetic disorder caused from mutations in the Cadherin 3 (CDH3) gene. Results In the present study, we reported an Iranian family with three affected members born to a consanguineous parent. Mutational analysis using whole exome sequencing has revealed a nucleotide change in CDH3 gene (NM_001793:exon8:c.830delG) which leads to a frame-shift mutation (p.G277Afs*20). No intra-familial phenotypic variation was found. Conclusion Identification of disease-causing mutation in this family facilitated the effective genetic counseling and prenatal diagnosis.

Autosomal Recessive Hypohidrotic Ectodermal Dysplasia Caused by a Novel Mutation in EDAR Gene

Backgrounds: Hypohidrotic ectodermal dysplasia (HED) is a rare genetic disorder, distinguished by hypotrichosis, hypohidrosis, and hypodontia. HDE can be inherited in X-linked recessive manner as a result of mutations in the ectodysplasin A (EDA) gene as well as autosomal dominant and autosomal recessive manners both of them caused by mutations in EDA receptor (EDAR) and EDAR-associated death domain (EDARADD) genes.Findings: In this report, we investigated a consanguineous Iranian family with autosomal recessive form of HED. A homozygous missense mutation was detected in exon 1 of EDAR gene in the proband (c.278C>G) resulting in p.C93S that alters the sequence of the EDAR protein. Conclusions: We facilitated the effective genetic counseling and prenatal diagnosis in this family through detection of the disease causing mutation.

Neurodegeneration with brain iron accumulation 2A: Report of four independent cases

Neurodegeneration with brain iron accumulation-2A (NBIA2A, also called infantile neuroaxonal dystrophy) is an autosomal recessive disorder of the central nervous system (CNS) caused by mutations in PLA2G6 gene. The characteristic features of NBIA2A are progressive course of mental and motor regression, cerebellar ataxia, hypotonia, spastic tetraplegia, hyperreflexia and visual defects. In the present study we report four independent cases of NBIA2A whose genetic defects have been identified through whole exome sequencing. Three novel mutations and a previously reported mutation have been detected in PLA2G6 gene in these patients. Identification of these mutations facilitated effective genetic counseling and prenatal diagnosis in the families.

OP22.08: Integrating ultrasound findings with chromosomal microarray stretches of homozygosity and principles in founder populations

Chromosomal microarray (CMA) analysis is effectively applied prenatally to detect copy number changes. SNP probes included on the microarray platform can detect regions of excessive homozygosity (ROH) and identical-by-descent genomic stretches. The utility of the latter in prenatal diagnosis is not well established. Recessive founder mutations have been identified within distinct ethnic groups. Combining these data with prenatal sonography provides accurate molecular diagnoses quickly. Three gravidae presenting with specific fetal sonographic findings: 1) ventriculomegaly with encephalocele; 2) severe polyhydramnion, and 3) enlarged echogenic kidneys, underwent amniocentesis for CMA, and Genome-Wide Human SNP array was used to analyse DNA from amniocytes. The Genomic Oligoarray and SNP array evaluation tool v3.0 was used to detect recessive loci associated with the reported clinical findings. Candidate regions were further interrogated using the National Genetic Database. Three fetuses from three distinct nuclear families in which the parents shared a similar ethnicity (either Ashkenazi or Bukharan Jews) but no reported consanguinity, were assessed. No copy number changes were observed, however evaluation of regions of homozygosity revealed a relevant candidate gene for the specific phenotype for each fetus. Using the National Genetic Database a specific mutation was examined in both parents (c.1167dupA mutation in the FKTN gene, c.167ins6[TTTCCC] mutation in the BSND gene and c.3761_3762delCCinsG in the PKHD1 gene, respectively). Both parents were found to be carriers and the fetuses homozygotes to the mutation. For the first time, specific sonographic pathology, data from ROH extracted from CMA results, and information regarding common founder mutations in distinct ethnic subgroups were combined to create a comprehensive streamlined approach to provide effective genetic diagnosis and counselling within the time constraints of ongoing pregnancy.

Bleeding is not the main clinical issue in many patients with inherited thrombocytopaenias.

Bleeding diathesis has been considered for a long time the main clinical issue impacting the lives of patients affected by inherited thrombocytopaenias. However, the number of known inherited thrombocytopaenias greatly increased in recent years, and careful evaluation of hundreds of patients affected by these 'new' disorders revealed that most of them are at risk of developing additional life-threatening disorders during childhood or adult life. These additional disorders are usually more serious and dangerous than low platelet count. For instance, it is known that mutations in RUNX1, ANKRD26 and ETV6 cause congenital thrombocytopaenia, but we now know that they also predispose to haematological malignancies. Similarly, MYH9 mutations result in congenital thrombocytopaenia and increase the risk of developing kidney failure, cataracts and hearing loss at a later stage, while MPL mutations cause a congenital thrombocytopaenia that almost always evolves into deadly bone marrow failure. Thus, identification of patients with these disorders is essential for evaluation of their prognosis, enabling effective genetic counselling, personalizing follow-up and giving appropriate treatments in case of development of additional diseases. Careful clinical evaluation and peripheral blood film examination are extremely useful tools in guiding the diagnostic process and identifying the candidate genes to be sequenced.

An analysis of the mutation in GJB2，GJB3，SLC26A4 and mtDNA12SrRNA in new born

Objective:To analyze deafness gene mutation in GJB2，GJB3，SLC26A4 and mtDNA12SrRNA in newborn and to explore the significance of genetic test and potential correlations between the genotype and clinical phenotype.Method:Blood samples were collected with a standard protocol and DNA templates are extracted from 501 newborn in Longgang of Shenzhen.MALDI-TOF-MS Technology was used to detect the coding region twenty mutations sites of GJB2，GJB3，SLC26A4 AND mtDNA12SrRNA，includingSLC26A4(1226G>A,1229C>T,281C>T,589G>A,IVS7-2A>T,1174A>T,IVS15+5G>A,1975G>C,2027T>A,2162C>T,2168A>G),GJB2(176-191del16,35delG,167delT,235 delC,299-300 delAT),GJB3(547G>A,538C>T),mtDNA12SrRNA(1555A>G,1494C>T).While two-step hearing screening was carried by using AABR（automatedauditory brainstem response）and DPOAE. Result:In the 501 newborns,26 cases were found have one or two allele mutations of deafness-susceptibility genes.GJB2 gene mutation(n=9,1.796%) all were 235 delC single heterozygosity mutation.GJB3 gene mutation(n=3,0.599%). SLC26A4 gene mutation(n=12,2.395%) included IVS7-2A>G heterozygosity mutation(n=5). MtDNA 12Rrna gene mutation was found in 3 child(n=3,0.599%). Finally one of 26 infants was diagnosed enlarged vestibular aqueduct syndrome. The infant was detected 2168A>G heterozygosity mutation. Conclusion:235delC is the main mutation form of GJB2 gene,while it is the hottest mutation in People. But SLC26A4 gene mutations are the main type in newborn. MtDNA 12Rrna gene mutation was found in 3 child.This genetic epidemiological study demonstrated that genetic screening is helpful for determining high risk individuals and early discovering possible late-onset hearing loss. Moreover pationts and family member can acquire more effective genetic counseling.

Two Cases of X-linked Liver Glycogenosis in Hunan Province: Transmission from the Undiagnosed Maternal Grandfather

X-linked liver glycogenosis (XLG), also known as glycogen storage disease (GSD) type-IXa, is characterized by hepatomegaly, abnormal liver functions and growth retardation. This disease is a result of a deficiency of hepatic phosphorylase kinase (PHK), which plays an important role in glycogen metabolism by activating phosphorylase. We aim at identifying the genetic cause of the GSD running in a family with two affected boys, and hence develop proper management and genetic counseling. The boys presented with typical GSD signs and symptoms. The histology of the liver biopsy from the old brother showed glycogen accumulation in hepatocytes and confirmed his condition of GSD. The younger brother did not have a biopsy. Whole exome sequencing was used to analyze the genetic structure of the proband patients and their parents. Sanger sequencing was used to validate and confirm the identified mutation. The results showed that there was a known pathogenic mutation (p.E1125K) in PHKA2 gene located on chromosome Xp22, which encodes the regulatory subunit of PHK. Pedigree analysis revealed that the mother was a carrier, and the disease of both brothers was transmitted through their undiagnosed maternal grandfather. This is the first report of XLG caused by this mutation in China, and it indicated that GSD may be undiagnosed or underestimated since GSD IXa is one of the mild form of glycogenosis in terms of clinical symptoms. However, it is necessary to identify the genetic cause in order to perform effective intervention and genetic counseling.

CLINICAL AND GENETIC CHARACTERISTICS OF MUCOLIPIDOSIS II AND IIIA TYPES IN CHILDREN

The article is devoted to a rare pathology from a group of accumulation diseases with an autosomal recessive type of inheritance – mucolipidosis II and IIIA types. The disease is characterized by a greater phenotypic similarity to mucopolysaccharidosis. Objective: analysis of genophenotypic parameters in Russian patients with mucolipidosis II and IIIA types. The activity of lysosomal enzymes in plasma (β-glucuronidase, total hexosaminidase and N-acetyl-α-D-glucosaminidase) was measured using a standard technique using chromogenic and fluorogenic substrates. Genomic DNA of peripheral blood leukocytes was isolated using a set of reagents Preb 100 (DIAtomTM). Amplification of all exons of the GNPTAB gene was carried out by polymerase chain reaction (PCR) followed by direct non-radioactive sequencing by Sanger. 50 patients aged from 1.5 to 10 years were examined. The clinical symptoms of the disease included: a Hurler-like phenotype, growth retardation, skeletal, cardiac and vascular damage, and CNS. Mucolipidosis type II (I-cell disease) was characterized by a more severe course. The clinical diagnosis was confirmed by the results of laboratory methods of investigation: normal parameters of renal excretion of glycosiminoglycans (GAG), high (5-15 times higher than normal) activity of lysosomal hydrolases in blood plasma and detection of mutations in the GNPTAB gene. 35 probands are completely genotyped. In 8 patients only 8 mutant alleles were detected; 7 mutations were not detected. Six new mutations in exons 1 (p.I31N; p.Q36P), 10 (p.L398P), 11 (p.W446X) and 13 (p.S738X; c.2250delT) were found, including a frequent mutation for Russian patients P.S738X (21% alleles). The most common (31.4% alleles) in the Russian cohort of patients was a known small deletion c. 3503_3504delTC, leading to a reading frameshift. A clinical observation of a child with type 2 mucolipidosis (I-cell disease) with typical symptomatology of the disease caused by two nonsense mutations of the GNPTAB gene is presented: p.S738X / p.R375X. In conclusion, it is emphasized that the identification of mutations of the GNPTAB gene provides prediction of the severity of the disease course, an understanding of the mechanisms of its development that will contribute to the development of pathogenetic treatment methods, improving the quality of life of patients and effective medical and genetic counseling.

Mothers' Knowledge and Practices for their Children with Sickle Cell Anemia At New Valley Governorate Hospitals

Sickle cell disease (SCD) is a genetic blood disorder associated with multiple health complications including anemia and recurrent pain episodes. Objectives: This study aimed to assess the mothers' knowledge and practices for children with SCA at New Valley governorate hospitals. Design: A descriptive research design was utilized in this study. Subjects and method: This study included 45 mothers of children who were diagnosed with SCA. Setting This study was conducted in the inpatient pediatric unit and pediatric clinics at New Valley governorate hospitals. Tool: A structured interview sheet was utilized to collect the necessary data. Results: It was found that more than one third (40% ) of mothers had satisfactory knowledge. Slightly more than one third of mothers, (35.6%) had poor knowledge about SCA. It was found that half of mother's (51.1%) had satisfactory level of practice, while 48.9% had unsatisfactory level of practice regarding SCA. conclusion the low level of maternal education was a significant risk factor for the poor knowledge and poor practices of the mothers regarding management of SCA. Recommendations: Effective genetic counseling, neonatal screening test should be applied at the New valley governorate hospitals for early detection of SCA, and health education program sessions for mothers of children with SCA.

In silico, in vitro and case-control analyses as an effective combination for analyzing BRCA1 and BRCA2 unclassified variants in a population-based sample

Ascertaining the clinical consequences of BRCA1 and BRCA2 variants of uncertain significance (VUS) is currently indispensable for providing effective genetic counseling and preventive actions for families with hereditary breast and ovarian cancer (HBOC). To this end, we conducted a combination of in silico prediction and cDNA splicing analyses of 13 BRCA1 and 10 BRCA2 VUS identified in our cohort as well as a case-control analysis in a population-based sample of 10 recurrent VUS. We observed consistent results between the in silico predictions and sequencing analyses for all analyzed VUS. An abnormal cDNA pattern was observed for variants c.212+1G>A and c.5278-1G>A in BRCA1 and c.516+2T>A and c.8168A>G in BRCA2 according to in silico splicing prediction. A case-control study of VUS confirmed the polymorphisms of the c.67+62A>G, c.7008-62A>G and c.8851G>A BRCA2 variants previously published. c.4068G>A in the BRCA2 gene can also be considered a polymorphism due to its occurrence at a frequency greater than 1% in our population. Our study shows that employing population-based analysis and a combination of several in silico methods yields highly accurate information, resulting in a reliable tool for selecting variants for cDNA sequencing analysis in routine cancer genetic counseling units.

Abstract 5286: A pipeline for developing a novel, predictive tool to classify variants of uncertain significance (VUS) in Lynch Syndrome

Abstract Lynch syndrome (LS) highly predisposes individuals and their families to an increased risk of colorectal cancers and to cancers of the endometrium, ovary, gastrointestinal tract, pancreas, upper urinary tract, and other tissues. The occurrence of LS has been attributed to germline, heterozygous mutations in four genes in the DNA mismatch repair (MMR) pathway: MLH1, MSH2, MSH6 and PMS2. Mutations in the MLH1 and MSH2 genes account for the majority of detectable mutations in LS, with more infrequent mutations in MSH6 and PMS2. Clinical diagnosis of LS helps direct the management of the disease and risk assessment for future cancers in the family. A major challenge is the determination of variant pathogenicity in MMR genes, particularly those that code for missense mutations. According the InSiGHT database, there are &amp;gt;5000 unclassified variants of unknown significance (VUS), and this number continues to grow every day due to the increased prevalence of genomic testing. Such VUS present an enormous challenge to effective genetic counseling of LS families. There are numerous predictive methods, such as SIFT and Polyphen-2, for predicting the effects of missense mutations in any gene including LS genes. Further, there is a great deal of promise for gene-specific predictors, such as PON-MMR and CoDP, that are trained on the physical and evolutionary features of known deleterious and benign mutations in the target genes of interest. Since the number of available mutations for the LS genes with experimental phenotypes is limited, we have developed and applied a pipeline to perform experimental validation of VUS in MMR genes. MMR genes with introduced VUS were assessed in vitro in comparison to wild type genes for the effect of the VUS on steady state protein expression, localization, and functionality in inducing DNA damage checkpoints and influencing cell survival following treatment with a panel of DNA-damaging agents. We then assessed a panel of VUS in MSH2, MLH1 and PMS2 in HEK293 kidney cells and colorectal cancer (CRC) cell lines bearing deletions in the MMR genes being tested. This mid-throughput pipeline allowed effective validation of the functional consequences of each VUS, generating additional data to enhance the efficacy of gene-specific predictors for the LS genes that we are developing. Such tools may greatly benefit the assessment of MMR gene variants identified through genetic testing and for genetic counseling of LS families. Citation Format: Sanjeevani Arora, Peter J. Huwe, Rahmat Sikder, Manali Shah, Sanat Deshpande, Michael J. Hall, Roland L. Dunbrack, Erica A. Golemis. A pipeline for developing a novel, predictive tool to classify variants of uncertain significance (VUS) in Lynch Syndrome. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5286.

Role of molecular testing in the multidisciplinary diagnostic approach of ichthyosis.

BackgroundThe term ichthyosis describes a generalized disorder of cornification characterized by scaling and/or hyperkeratosis of different skin regions. Mutations in a broad group of genes related to keratinocyte differentiation and epidermal barrier function have been demonstrated to play a causative role in disease development. Ichthyosis may be classified in syndromic or non-syndromic forms based on the occurrence or absence of extracutaneous signs. In this setting, the diagnosis of ichthyosis is an integrated multistep process requiring a multidisciplinary approach in order to formulate the appropriate diagnostic hypothesis and to address the genetic testing.MethodsDue to the complex features of the different ichthyoses and the high number of genes involved we have investigated a group of 64 patients, affected by syndromic and non-syndromic diseases, using Next Generation Sequencing as a new tool for the molecular diagnosis.ResultsUsing this innovative molecular approach we were able to find pathogenic mutations in 53 out of 64 patients resulting in 82.8 % total detection rate. An interesting result from the analysis of the data is the high rate of novel sequence variations found compared to known mutations and the relevant rate of homozygous mutations.ConclusionsThe possibility to analyze a large number of genes associated with various diseases allows to study cases with phenotypes not well-determined, giving the opportunity to make new genotype-phenotype correlation. In some cases there were discrepancies between clinical features and histology or electron microscopy and only molecular analysis allowed to definitively resolve the diagnostic dilemma. The genetic diagnosis of ichthyosis leads to a more accurate and effective genetic counseling, allowing correct evaluation of the risk of recurrence, particularly in families with consanguineous background.Electronic supplementary materialThe online version of this article (doi:10.1186/s13023-016-0384-4) contains supplementary material, which is available to authorized users.