Parental Segregation Study Reveals Rare Benign and Likely Benign Variants in a Brazilian Cohort of Rare Diseases

Genomic studies may generate massive amounts of data, bringing interpretation challenges. Efforts for the differentiation of benign and pathogenic variants gain importance.In this article, we used segregation analysis and other molecular data to reclassify to benign or likely benign several rare clinically curated variants of autosomal dominant inheritance from a cohort of 500 Brazilian patients with rare diseases.This study included only symptomatic patients who had undergone molecular investigation with exome sequencing for suspected diseases of genetic etiology. Variants clinically suspected as the causative etiology and harbored by genes associated with highly-penetrant conditions of autosomal dominant inheritance underwent Sanger confirmation in the proband and inheritance pattern determination because a “de novo” event was expected.Among all 327 variants studied, 321 variants were inherited from asymptomatic parents. Considering segregation analysis, we have reclassified 51 rare variants as benign (n=51) and 211 as likely benign (n=211).In our study, the inheritance of a highly penetrant variant expected to be de novo for pathogenicity assumption was considered as a non-segregation and, therefore, a key step for benign or likely benign classification. Studies like ours may help to identify rare benign variants and improve the correct interpretation of genetic findings.

Familial Segregation of Venous Thromboembolism in Sweden: A Nationwide Family Study of Heritability and Complex Segregation Analysis

Background This is the first nationwide segregation analysis that aimed to determine whether familial venous thromboembolism (VTE) is attributable to inheritance and/or shared environment, and the possible mode of inheritance. Methods and Results The Swedish Multi‐Generation Register was linked to the Swedish patient register for the period 1964 to 2015. Three generational families of Swedish‐born individuals were identified. Heritability was examined using Falconer regression. Complex segregation analysis was conducted using the Statistical Analysis for Genetic Epidemiology software (version 6.4, 64‐bit Linux). Among the 4 301 174 relatives from 450 558 pedigrees, 177 865 (52% women) individuals were affected with VTE. VTE occurred in 2 or more affected relatives in 61 217 (13.6%) of the pedigrees. Heritability showed age and sex dependence with higher heritability for men and young individuals. In 18 933 pedigrees, VTE occurred only in the first generation and was not inherited. Segregation analysis was performed in the remaining 42 284 pedigrees with inherited VTE and included 939 192 individuals. Prevalence constraints were imposed in the models to allow for the selection of the pedigrees analyzed. The sporadic nongenetic model could be discarded. The major‐type‐only model, with a correlation structure compatible with some polygenic effects, was the preferred model. Among the Mendelian models, the mixed codominant (plus polygenic) model was preferred. Conclusions This nationwide segregation analysis of VTE supports a genetic cause of the familial aggregation of VTE. Heritability was higher for men and younger individuals, suggesting a Carter effect, in agreement with a multifactorial threshold inheritance.

Evidence for hexasomic inheritance in Chrysanthemum morifolium Ramat. based on analysis of EST-SSR markers

Chrysanthemums (Chrysanthemum morifolium Ramat.) are ornamental flowers, which are famous worldwide. The mode of inheritance has great implications for the genetic analysis of polyploid species. However, genetic analysis of chrysanthemum has been hampered because of its controversial inheritance mode (disomic or hexasomic). To classify the inheritance mode of chrysanthemums, an analysis of three approaches was carried out in an F1 progeny of 192 offspring using 223 expressed sequence tag-simple sequence repeat (EST-SSR) markers. The analysis included segregation analysis, the ratio of simplex marker alleles linked in coupling to repulsion, as well as the transmission and segregation patterns of EST-SSR marker alleles. After segregation analysis, 204 marker alleles fit hexasomic inheritance and 150 marker alleles fit disomic inheritance, showing that marker alleles were inherited predominantly in a hexasomic manner. Furthermore, the results of the analysis of allele configuration and segregation behavior of five EST-SSR markers also suggested random pairing of chromosomes. Additionally, the ratio of simplex marker alleles linked in coupling to repulsion was 1:0, further supporting hexasomic inheritance. Therefore, it could be inferred that chrysanthemum is a complete or near-complete hexasome.

Parental segregation study reveals rare benign and likely benign variants in a Brazilian cohort of rare diseases

Genomic studies may generate massive amounts of data, bringing interpretation challenges. Efforts for the differentiation of benign and pathogenic variants gain importance. In this article, we used segregation analysis and other molecular data to reclassify to benign or likely benign several rare clinically curated variants of autosomal dominant inheritance from a cohort of 500 Brazilian patients with rare diseases. This study included only symptomatic patients who had undergone molecular investigation with exome sequencing for suspected diseases of genetic etiology. Variants clinically suspected as the causative etiology and harbored by genes associated with highly-penetrant conditions of autosomal dominant inheritance underwent Sanger confirmation in the proband and inheritance pattern determination because a “de novo” event was expected. Among all 327 variants studied, 321 variants were inherited from asymptomatic parents. Considering segregation analysis, we have reclassified 51 rare variants as benign (n=51) and 211 as likely benign (n=211). In our study, the inheritance of a highly penetrant variant expected to be de novo for pathogenicity assumption was considered as a non-segregation and, therefore, a key step for benign or likely benign classification. Studies like ours may help to identify rare benign variants and improve the correct interpretation of genetic findings.

Paternal Uniparental Isodisomy of Chromosome 2 in a Patient with CNGA3-Associated Autosomal Recessive Achromatopsia

Achromatopsia (ACHM) is a rare autosomal recessively inherited retinal disease characterized by congenital photophobia, nystagmus, low visual acuity, and absence of color vision. ACHM is genetically heterogeneous and can be caused by biallelic mutations in the genes CNGA3, CNGB3, GNAT2, PDE6C, PDE6H, or ATF6. We undertook molecular genetic analysis in a single female patient with a clinical diagnosis of ACHM and identified the homozygous variant c.778G>C;p.(D260H) in the CNGA3 gene. While segregation analysis in the father, as expected, identified the CNGA3 variant in a heterozygous state, it could not be displayed in the mother. Microsatellite marker analysis provided evidence that the homozygosity of the CNGA3 variant is due to partial or complete paternal uniparental isodisomy (UPD) of chromosome 2 in the patient. Apart from the ACHM phenotype, the patient was clinically unsuspicious and healthy. This is one of few examples proving UPD as the underlying mechanism for the clinical manifestation of a recessive mutation in a patient with inherited retinal disease. It also highlights the importance of segregation analysis in both parents of a given patient or especially in cases of homozygous recessive mutations, as UPD has significant implications for genetic counseling with a very low recurrence risk assessment in such families.

P–083 Analysis of chromosomal segregation and interchromosomal effects (ICE) in sperms from balanced translocation carriers using fluorescence in situ hybridization (FISH) after sperm selector separation

Study question Influence of sperm selector separation of sperms on their translocation load, segregation pattern, motility and occurrence of interchromosomal effects Summary answer Sperm selector separation led to reduction of the translocation load, shift in segregation pattern and lower rates of interchromosomal effects within sperm samples What is known already Balanced translocations in men are known to be one of the main causes of reproductive failure. The segregation pattern in sperms is determined by the distribution of the chromosomes during meiosis. Interchromosomal effects can also influence the distribution of chromosomes that are not involved in the translocation. The sperm selector used consists of two concentric chambers, which are overlaid by a U-ring and a cover glass. Motile sperms migrate from the native ejaculate in the medium filled inner chamber by using a capillary bridge created by the U-ring. This avoids potential harmful centrifugation and allows accumulation of motile sperms. Study design, size, duration Twenty-one carriers of balanced translocations participated in the study. In addition, 15 patients were involved as control. All participants signed an informed consent (F–8–15). Samples of three patients did not meet the internal quality criteria and had to be excluded from analysis. The study started in 2015 and is still ongoing. Participants/materials, setting, methods Liquefied native ejaculate was processed with a sperm selector. Native ejaculate, non-migrated sperms from the outer chamber and migrated sperms from the inner chamber were transferred onto glass slides, fixed and underwent a decondensation treatment. For segregation analysis FISH translocation specific FISH probe mixes were used and tested on patient’s blood. Interchromosomal effects were analysed with FISH probes for the chromosomes X, Y, 18 and 13, 21. Evaluation was done manually using fluorescence microscopy. Main results and the role of chance Segregation analysis was done for more than 25,000 sperms from men carrying a balanced translocation (18 patients with reciprocal and 3 patients with Robertsonian translocation). Separation via sperm selector led to a reduction in translocation load (native to separated approach 49,1±11,5% to 34,8±9,4% (P = <0,01), the rate depending on the specific translocation. There was also a shift in the segregation pattern, which seemed to be influenced by the specific translocation and the resulting steric alignment of the corresponding quadrivalent / trivalent. Additionally, more than 90,000 sperms from patients with balanced translocations were analysed for interchromosomal effects. Separation led to reduced maldistribution rate (native to separated approach 7,1±3,5% to 5±3,1%, P = <0,01) whereas the steric alignment of the corresponding quadrivalent / trivalent seems to influence the interchromosomal effect as well. For control, sperms from control patients were analysed regarding the chromosomes X, Y, 18 and 13, 21. In about 90,000 control sperms separation led to reduced maldistribution rate (native to separated approach 5,4±1,5% to 3,8±1,1%; P = <0,01). Limitations, reasons for caution The number of accumulated strandbreak-free sperms depended on the motility and sperm count of the native ejaculate. Examinations are not reproducible, as each sample delivery is influenced by external circumstances Wider implications of the findings: Sperm selector separation can be used before ART to reduce the translocation load and rate of maldistribution in sperms from carriers of balanced translocations. This could have a considerable impact on PGT results after trophectoderm biops. Trial registration number Not applicable