Genetic Counseling Of Families Research Articles

A Novel Missense Variant of TP63 Heterozygously Present in Split-Hand/Foot Malformation

Background Split-hand/foot malformation (SHFM) is a severe congenital disability mainly characterized by the absence or hypoplasia of the central ray of the hand/foot. To date, several candidate genes associated with SHFM have been identified, including TP63, DLX5, DLX6, FGFR1, and WNT10B. Herein, we report a novel variant of TP63 heterozygously present in affected members of a family with SHFM. Methods This study investigated a Chinese family, in which the proband and his son suffered from SHFM. The peripheral blood sample of the proband was used to perform whole-exome sequencing (WES) to explore the possible genetic causes of this disease. Postsequencing bioinformatic analyses and Sanger sequencing were conducted to verify the identified variants and parental origins on all family members in the pedigree. Results By postsequencing bioinformatic analyses and Sanger sequencing, we identified a novel missense variant (NM_003722.4:c.948G>A; p.Met316Ile) of TP63 in this family that results in a substitution of methionine with isoleucine, which is probably associated with the occurrence of SHFM. Conclusion A novel missense variant (NM_003722.4:c.948G>A; p.Met316Ile) of TP63 in SHFM was thus identified, which may enlarge the spectrum of known TP63 variants and also provide new approaches for genetic counselling of families with SHFM.

Cancer Predisposition Syndromes Associated With Pediatric High-Grade Gliomas.

Pediatric High-Grade Gliomas (pHGG) are among the deadliest childhood brain tumors and can be associated with an underlying cancer predisposing syndrome. The thorough understanding of these syndromes can aid the clinician in their prompt recognition, leading to an informed genetic counseling for families and to a wider understanding of a specific genetic landscape of the tumor for target therapies. In this review, we summarize the main pHGG-associated cancer predisposing conditions, providing a guide for suspecting these syndromes and referring for genetic counseling.

Federal clinical guidelines. Primary immunodeficiency: severe combined immunodeficiency

Severe combined immunodeficiency (SCID) is the most life-threatening form of primary immunodeficiency, fatal within the first years of life if hematopoietic stem cell transplantation (HSCT) is not performed. Early diagnosis is crucial for prevention of multiple life-threatening complications, which in turn allows for successful HSCT. Current publication contains clinical recommendations for diagnosis of SCID and its complications, complex treatment, including HSCT, prenatal diagnostics and genetic family counselling.

Yield and Utility of Germline Testing Following Tumor Sequencing in Patients With Cancer

Both germline genetic testing and tumor DNA sequencing are increasingly used in cancer care. The indications for testing and utility of these 2 tests differ, and guidelines recommend that germline analysis follow tumor sequencing in certain patients to determine whether particular variants are of somatic or germline origin. Broad clinical experience with such follow-up testing has not yet been thoroughly described. To examine the yield and utility of germline testing following tumor DNA sequencing in a large, diverse patient population. A retrospective cohort study examined germline testing through a laboratory supporting multiple academic and community clinics. Participants included 2023 patients with cancer who received germline testing and previously underwent tumor DNA sequencing. These patients received germline testing between January 5, 2015, and January 31, 2020, although most (81% of patients) received testing between January 2, 2018, and January 31, 2020. The prevalence of pathogenic germline variants (PGVs) was calculated by gene, cancer type, and age at diagnosis. Potential actionability of these findings was determined based on current management guidelines, precision therapy labels, and clinical trial eligibility criteria. Patient records were reviewed to determine whether germline follow-up testing would have been recommended by current guidelines. Among 2023 eligible patients, 1085 were female (53.6%), and the median age at cancer diagnosis was 56 (range, 0-92) years. Pathogenic germline variants were detected in 617 patients (30.5%; 95% CI, 28.5%-32.6%) and were prevalent across patient ages (1-85 years) and cancer types, including cancers known to be strongly associated with germline variance (eg, breast, colorectal) as well as others (eg, renal, lung, and bladder). Many patients (78%-82%) with PGVs met criteria for germline follow-up testing, and 8.1% of PGVs were missed by tumor sequencing. Among those with germline-positive findings, 69 patients (11.2%) had PGVs identified only after presenting with a second primary cancer that possibly could have been detected earlier or prevented given current gene-specific surveillance and risk-reduction recommendations. The findings of this study suggest that germline analysis following tumor sequencing often produces findings that may impact patient care by influencing systemic therapy choices, surgical decisions, additional cancer screening, and genetic counseling in families. Current guidelines and tumor testing approaches appear to capture many, but not all, of these germline findings, reinforcing the utility of both expanded germline follow-up testing as well as germline analysis independent of tumor sequencing in appropriate patients.

Biallelic Pathogenic GFRA1 Variants Cause Autosomal Recessive Bilateral Renal Agenesis.

Congenital anomalies of the kidney and urinary tract (CAKUT) are one of the most common malformations identified in the fetal stage. Bilateral renal agenesis (BRA) represents the most severe and fatal form of CAKUT. Only three genes have been confirmed to have a causal role in humans (ITGA8, GREB1L, and FGF20). Genome sequencing within a diagnostic setting and combined data repository analysis identified a novel gene. Two patients presented with BRA, detected during the prenatal period, without additional recognizable malformations. They had parental consanguinity and similarly affected, deceased siblings, suggesting autosomal recessive inheritance. Evaluation of homozygous regions in patient 1 identified a novel, nonsense variant in GFRA1 (NM_001348097.1:c.676C>T, p.[Arg226*]). We identified 184 patients in our repository with renal agenesis and analyzed their exome/genome data. Of these 184 samples, 36 were from patients who presented with isolated renal agenesis. Two of them had loss-of-function variants in GFRA1. The second patient was homozygous for a frameshift variant (NM_001348097.1:c.1294delA, p.[Thr432Profs*13]). The GFRA1 gene encodes a receptor on the Wolffian duct that regulates ureteric bud outgrowth in the development of a functional renal system, and has a putative role in the pathogenesis of Hirschsprung disease. These findings strongly support the causal role of GFRA1-inactivating variants for an autosomal recessive, nonsyndromic form of BRA. This knowledge will enable early genetic diagnosis and better genetic counseling for families with BRA.

Huntington’s disease

Huntingtons disease is one of the most common hereditary neurodegenerative diseases, which remains practically incurable, inevitably leading to the disability of patients and premature death. A fairly wide prevalence in the world, the special severity of the course, the almost complete penetrance of the mutant gene, the peculiarity of clinical and genetic correlations in Huntingtons disease have attracted researchers specializing in neuroscience for many years. The study of the molecular neurobiology of Huntingtons disease over the past decades has largely contributed to significant progress in molecular biology, genetics, and many other biomedical disciplines. At the same time, Huntingtons disease has become a model disease in resolving issues of genetic counseling and prognostic testing in modern medical genetics. The review provides brief facts on the history of the study of the disease, including mapping and identification of the mutant gene. The issues of etiology and pathogenesis, molecular genetics of the disease, epidemiology, diagnostics, and differential diagnostics are discussed in detail. The spectrum of clinical manifestations of Huntingtons disease, its various forms, and course features are presented. From a modern perspective, the problem of developing valid biomarkers of both the manifest and the asymptomatic stages of the disease, as well as the course of the pathological process, are highlighted. The main issues of primary and secondary prevention of Huntingtons disease, bioethical principles of conducting genetic counseling for families burdened by this disease are outlined. The approaches to the symptomatic treatment of Huntingtons disease are described, a review of the main promising experimental therapeutic methods that can potentially slow down or stop the progression of the disease, as well as prevent its manifestation in asymptomatic carriers of the mutant gene, are presented. An important contribution of patient organizations to addressing issues affecting the interests of burdened families, scientific and clinical research on the disease was noted. Literature was searched and analyzed using the databases of Scopus, Web of Science, Pubmed (MedLine), eLibrary.

COVID-19’s Impact on Genetics at One Medical Center in New York

COVID-19’s Impact on Genetics at One Medical Center in New York

Patterns of cancer family history and genetic counseling eligibility among African Americans with breast, prostate, lung, and colorectal cancers: A Detroit Research on Cancer Survivors cohort study.

Family history (FH) remains one of the strongest risk factors for many common cancers and is used to determine cancer genetic counseling (CGC) eligibility, but the understanding of familial cancer patterns in African Americans is limited. This study evaluated cancer FH among African Americans with invasive breast cancer, prostate cancer, lung cancer, or colorectal cancer (CRC) in the Detroit Research on Cancer Survivors (ROCS) cohort. Associations between participant cancer type, site-specific FH, and meeting national guidelines for CGC were evaluated via logistic regression. Cancer FH patterns were evaluating via hierarchical clustering. Among 1500 ROCS participants, 71% reported at least 1 first-degree relative or grandparent with cancer. FHs of breast cancer, CRC, lung cancer, and prostate cancer were most common among participants with the same diagnosis (odds ratio [OR] for breast cancer, 1.14; P<.001; OR for CRC, 1.08; P=.003; OR for lung cancer, 1.09; P=.008; OR for prostate cancer, 1.14; P<.001). Nearly half of the participants (47%) met national CGC guidelines, and 24.4% of these participants met CGC criteria on the basis of their cancer FH alone. FH was particularly important in determining CGC eligibility for participants with prostate cancer versus breast cancer (OR for FH vs personal history alone, 2.91; 95% confidence interval, 1.94-4.35; P<.001). In clustering analyses, breast and prostate cancer FH-defined clusters were common across all participants. Clustering of CRC and breast cancer FHs was also observed. ROCS participants reported high rates of cancer FH. The high rate of eligibility for CGC among ROCS participants supports the need for interventions to increase referrals and uptake of CGC among African Americans.

Genetic Counseling for Families with Sporadic Intellectual Disability in North of Iran: A Retrospective Study

Background Intellectual Disability (ID) is a heterogeneous disorder, in which at least 600 genes participate. The present study aimed to identify the effect of genetic counseling and consanguinity marriage in Iranian families with sporadic mental disability. Materials and Methods: In this retrospective cross-sectional study, we examined 151 families with a sporadic mental disability referred for genetic consultation to the Welfare Center of Sari city, North of Iran. Results: About 41.05% (n=62) of the cases were consanguinity marriage. In this study, other diseases were also observed with ID. The following four types of consultations were also reviewed, most of which were Diagnostic Counseling (DC) (60%). According to the inheritance pattern analysis, the share of non-hereditary cases was higher compared to the share of hereditary and unknown cases. The results of the present study showed a significant difference between consanguinity marriages and potential genetic etiology ID (P=0.012). Besides, there was no significant difference between other groups. Conclusion: In this study, we highlighted the importance of genetic counseling and found that consanguinity marriage was a key factor in the development of the disease in our society. Therefore, given the high cost of genetic tests and socio-economic problems, it is wise to include genetic counseling to prevent many diseases such as mental disability before birth.

Homozygous variants of EDAR underlying hypohidrotic ectodermal dysplasia in three consanguineous families.

Hypohidrotic ectodermal dysplasia (HED) is a congenital anomaly characterized by hypohydrosis, hypotrichosis and hypodontia. Mutations in at least four genes (EDAR, EDARADD, WNT10A, TRAF6) have been reported to cause both autosomal recessive and autosomal dominant forms of HED. Mutations in two other genes (EDA and IKBKG) have been reported to cause X-linked HED. To clinically characterize three consanguineous families (A-C) segregating with autosomal recessive HED and identify possible disease-causing variants of EDAR and EDARADD genes. The genes, EDAR and EDARADD, were sequenced in Family A and C, and exome sequencing was performed in Family B. Additionally, in Family A and C, the effect of the identified variants was examined by analysis of EDAR mRNA, extracted from hair follicles from both affected and unaffected members. Sequence analysis revealed three possible disease-causing EDAR variants including a novel splice acceptor site variant (IVS3-1G > A) in Family A and two previously reported mutations (p.[Ala26Val], p.[Arg25*]) in the two other families. Previously, the nonsense variant p.(Arg25*) was reported only in the heterozygous state. Analysis of the RNA, extracted from hair follicles, revealed skipping of a downstream exon in EDAR and complete degradation of EDAR mRNA in affected members in family A and C, respectively. Computational modelling validated the pathogenic effect of the two variants identified in Family B and C. The three variants reported here expand the spectrum of EDAR mutations associated with HED which may further facilitate genetic counselling of families segregating with similar disorders in the Pakistani population.

Secondary findings in inherited heart conditions: a genotype-first feasibility study to assess phenotype, behavioural and psychosocial outcomes

Disclosing secondary findings (SF) from genome sequencing (GS) can alert carriers to disease risk. However, evidence around variant-disease association and consequences of disclosure for individuals and healthcare services is limited. We report on the feasibility of an approach to identification of SF in inherited cardiac conditions (ICC) genes in participants in a rare disease GS study, followed by targeted clinical evaluation. Qualitative methods were used to explore behavioural and psychosocial consequences of disclosure. ICC genes were analysed in genome sequence data from 7203 research participants; a two-stage approach was used to recruit genotype-blind variant carriers and matched controls. Cardiac-focused medical and family history collection and genetic counselling were followed by standard clinical tests, blinded to genotype. Pathogenic ICC variants were identified in 0.61% of individuals; 20 were eligible for the present study. Four variant carriers and seven non-carrier controls participated. One variant carrier had a family history of ICC and was clinically affected; a second was clinically unaffected and had no relevant family history. One variant, in two unrelated participants, was subsequently reclassified as being of uncertain significance. Analysis of qualitative data highlights participant satisfaction with approach, willingness to follow clinical recommendations, but variable outcomes of relatives’ engagement with healthcare services. In conclusion, when offered access to SF, many people choose not to pursue them. For others, disclosure of ICC SF in a specialist setting is valued and of likely clinical utility, and can be expected to identify individuals with, and without a phenotype.

Silver-Russell syndrome. Clinical and etiopathological aspects of a model genomic imprinting entity.

Silver-Russell syndrome is characterized by asymmetrical intrauterine growth retardation, with normal head circumference and small, pointed chin, which results in a triangular face. It can also include body asymmetry, among other characteristics. Its global incidence is estimated at 1 in 30 000-100 000 births, even though this figure may be underestimated. In approximately 60 % of cases, a molecular cause can be identified, and the main one is hypomethylation of the paternal allele at the imprinting control region 1 located at 11p15.5-p15.4. It is necessary to make the diagnosis of this entity, exclude differential diagnoses, and know (epi)genotype-phenotype correlations in order to ensure an adequate follow-up, provide available therapeutic options, and offer a timely family genetic counseling. The objective of this article is to describe the current status of the Silver-Russell syndrome, a model of genomic imprinting disorder.

Functional evaluation of five BRCA2 unclassified variants identified in a Sri Lankan cohort with inherited cancer syndromes using a mouse embryonic stem cell-based assay

Next-generation sequencing of Sri Lankan families with inherited cancer syndromes resulted in the identification of five BRCA2 variants of unknown clinical significance. Interpreting such variants poses significant challenges for both clinicians and patients. Using a mouse embryonic stem cell-based functional assay, we found I785V, N830D, and K2077N to be functionally indistinguishable from wild-type BRCA2. Specific but mild sensitivity to olaparib and reduction in homologous recombination (HR) efficiency suggest partial loss of function of the A262T variant. This variant is located in the N-terminal DNA binding domain of BRCA2 that can facilitate HR by binding to dsDNA/ssDNA junctions. P3039P is clearly pathogenic because of premature protein truncation caused by exon 23 skipping. These findings highlight the value of mouse embryonic stem cell-based assays for determining the functional significance of variants of unknown clinical significance and provide valuable information regarding risk estimation and genetic counseling of families carrying these BRCA2 variants.

Adenocarcinoma de endometrio en una familia: variante de significado incierto en MSH6 en presencia de fenocopia, ¿cómo resolverlo?

Endometrial cancer (EC) is the second most common tumor in women with Lynch syndrome, and can be its first manifestation. It may exhibit negative immunostaining for DNA mismatch-repair proteins and/or microsatellite instability.We present the case of a woman with EC in which a MSH6 variant of unknown significance was identified. To establish the pathogenicity of the variant, the family study was extended, identifying her healthy sister as a carrier while her aunt, with EC, was not. In the latter, the histopathology of a first tumor block did not identify the pathway of carcinogenesis, but its repetition in a second tumor block suggested the possibility of it being a phenocopy.The multidisciplinary approach in the study of this family allowed a correct diagnosis of the different adenocarcinomas, adequate family genetic counselling and the correct assignment of pathogenicity to a variant in MSH6.

Анализ сегрегации хромосом у носителей реципрокных транслокаций

Аутосомные реципрокные транслокации (АРТ) приводят к повышенному риску образования несбалансированных гамет вследствие патологической сегрегации хромосом в мейозе у носителей. В настоящей статье приведены результаты анализа типов сегрегации для 26 АРТ, а также определены теоретически возможные варианты сегрегации хромосом. В 73% случаев у носителей АРТ в более, чем 50% бластомеров наблюдалось совпадение теоретического и детектируемого типов сегрегации. Полученные данные можно использовать для оптимизации персонализированного медико-генетического консультирования семей, где один из супругов является носителем АРТ, и имеющих репродуктивные проблемы, высокий риск неразвивающейся беременности и/или рождения ребенка с хромосомной патологией. Autosomal reciprocal translocations (ART) lead to an increased risk of imbalanced gametes formation due to pathological meiotic segregation. Segregation type was analyzed and theoretical segregation pattern was determined in 26 cleavage stage embryos in this article. A coincidence of theoretical and detectable segregation types was observed in more than 50 % of blastomeres in 73 % of cases. The data obtained may be used for personalized genetic counseling in families with high risks of recurrent spontaneous abortions, infertility or children with birth defects due to ART.

A GLI3 variant leading to polydactyly in heterozygotes and Pallister-Hall-like syndrome in a homozygote.

Variants in transcriptional activator Gli Kruppel Family Member 3 (GLI3) have been reported to be associated with several phenotypes including Greig cephalopolysyndactyly syndrome (MIM #175700), Pallister-Hall syndrome (PHS) (MIM #146510), postaxial polydactyly types A1 (PAPA1) and B (PAPB) (MIM #174200), and preaxial polydactyly type 4 (MIM #174700). All these disorders follow an autosomal dominant pattern of inheritance. Hypothalamic hamartomas (MIM 241800) is associated with somatic variants in GLI3. We report a related couple with parents having PAPA1 and PAPB, who had a fetus with a phenotype most compatible with PHS. Molecular analyses demonstrated homozygosity for a pathogenic GLI3 variant (c.1927C > T; p. Arg643*) in the fetus and heterozygosity in the parents. The genetic analysis in this family demonstrates that heterozygosity and homozygosity for the same GLI3 variant can cause a different phenotype. Furthermore, the occurrence of Pallister-Hall-like syndrome in a homozygous patient should be taken into account in genetic counseling of families with PAPA1/PAPB.

Identification of a recurrent nonsense mutation in HR gene responsible for atrichia with papular lesions in two Kashmiri families

Congenital atrichia (CA) is a rare form of irreversible alopecia with an autosomal recessive mode of inheritance. This form of hair loss is mainly associated with mutations in the human hairless (HR) gene located at chromosome 8p21.3. An additional unique feature atrichia with papular lesions (APL) comprises keratin-filled cysts known as papules. The present study aimed to uncover the underlying genetic causes of APL in two consanguineous Kashmiri families. In the present study, two consanguineous families of Kashmiri origin with APL displaying an autosomal recessive mode of inheritance were investigated. Whole exome and Sanger sequencing followed by bioinformatic studies, variant prioritization, Sanger validation and segregation analysis was performed to find the mutation. A recurrent nonsense (NM_005144: c.2818C > T:p.Arg940*) mutation was detected in exon 13 of the human HR gene. Whole exome sequencing analysis has widely been used in the screening of single gene disorders mutations, both in research and diagnostic laboratories. Sanger sequencing alone for genes such as HR becomes expensive and time consuming. Instead, it is recommended that a patient is to screen by whole exome sequencing and then special attention first focuses on known genes of the APL phenotype. This is helpful for intime diagnosis, being more efficient and economic. The results obtained in the present study may contribute to prenatal diagnosis, carrier secreening and the genetic counseling of families with the APL phenotype in Kashmiri poplution.

Novel loss‐of‐function mutation in MCM8 causes premature ovarian insufficiency

BackgroundPremature ovarian insufficiency (POI) is one major cause of female infertility, minichromosome maintenance complex component 8 (MCM8) has been reported to be responsible for POI.MethodsWhole‐exome sequencing was performed to identify the genetic variants of women with POI. Sanger sequencing was used to validate the variants in all the family members. Various bioinformatic software was used for the pathogenicity assessment. Reverse transcription polymerase chain reaction (RT‐PCR), real‐time quantitative PCR, and a chromosomal instability study induced by mitomycin C were performed to analyze the functional effects of the variant.ResultsA novel homozygous frameshift mutation (NM_032485.4:c.351_354delAAAG) of MCM8 gene was identified in the patients, segregated with POI in this family. This mutation is predicted to produce truncated MCM8 protein and to be pathogenic. Reverse transcription polymerase chain reaction revealed that the frameshift mutation led to a remarkably reduced level of MCM8 transcript products, and chromosomal instability study showed that the ability of mutant MCM8 to repair DNA breaks was impaired.ConclusionWe identified a novel homozygous frameshift mutation in the MCM8 gene in two affected sisters with POI, and functional analysis revealed that this mutation is pathogenic. Our findings enrich the MCM8 mutation spectrum and might help clinicians to make a precise diagnosis, thereby allowing better family planning and genetic counseling.

Clinical features of collagen VI-related dystrophies: A large Brazilian cohort

ObjectivesCollagen VI-related dystrophies (COL6-RDs) have a broad clinical spectrum and are caused by mutations in the COL6A1, COL6A2 and COL6A3 genes. Despite the clinical variability, two phenotypes are classically recognized: Bethlem myopathy (BM, milder form) and Ullrich congenital muscular dystrophy (UCMD, more severe form), with many patients presenting an intermediate phenotype. In this work, we present clinical and genetic data from 28 patients (27 families), aged 6–38 years (mean of 16.96 years), with COL6-RDs. Patients and methodsClinical, muscle histology and genetic data are presented. COL6A1, COL6A2 and COL6A3 genes were analyzed by next-generation sequencing (NGS). ResultsHomozygous or heterozygous variants were found in COL6A1 (12 families), COL6A2 (12 families) and COL6A3 (3 families). Patients with the severe UCMD phenotype (three cases) had a homogeneous clinical picture characterized by neonatal onset of manifestations, no gait acquisition and a stable course, but with severe respiratory involvement. Most of the patients with the mild UCMD phenotype had neonatal onset of manifestations (88.8 %), delayed motor development (66.6 %), slowly progressive course, pulmonary involvement (55.5 %) and loss of the walking capacity before the age of 10 (66.6 %). In the intermediate group (nine patients), some children had neonatal onset of manifestations (44.5 %) and delayed motor development (88.9 %); but all of them achieved the ability to walk and were still ambulatory. Some patients that had the BM phenotype presented neonatal manifestations (57.1 %); however, all of them had normal motor development and normal pulmonary function. Only one patient from the group of BM lost the walking capacity during the evolution of the disease. Other frequent findings observed in all groups were joint retractions, spinal deformities, distal hyperextensibility, congenital hip dislocation and keloid formation. ConclusionCOL6-RDs present variable clinical manifestations, but common findings are helpful for the clinical suspicion. NGS is a valuable approach for diagnosis, providing useful information for the genetic counseling of families.

Hereditary Nonpolyposis Colorectal Cancer HNPCC: From Diagnosis to Surgical Management of the Main Hereditary Form of Colorectal Cancer: A Review

Colorectal cancer (CRC) is the third most common cancer worldwide, the 5% of CRC are hereditary. Among hereditary forms of CRC the most frequent is Hereditary Nonpolyposis Colorectal Cancer (HNPCC). HNPCC is an autosomal dominant genetic disease. Molecular basis of HNPCC are linked to genetic alterations, involving several mismatch repair (MMR) genes. Diagnosis of HNPCC is frequently difficult: HNPCC diagnosis process starts from family medical history and genetic counselling and continue with molecular diagnosis and genetic tests which often identify MMR genes mutation. In HNPCC the role of screening is irreplaceable for prevention and early diagnosis of CRC and extracolic cancer, such as endometrium, ovary, urothelium, stomach, small bowel, pancreas, brain, biliary ducts neoplasms. Surgical management of HNPCC is significantly different between colonic and rectal cancer. The main problem in surgical approach for HNPCC patients is related to the possibility of developing metachronous colorectal cancer. The choice is always between extensive and segmental resection. The aim of this study is to give some practical indications to surgeons for the management of HNPCC patients.