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

2021 ◽  
Author(s):  
Caio Robledo Quaio ◽  
Jose Ricardo Magliocco Ceroni ◽  
Murilo Castro Cervato ◽  
Helena Strelow Thurow ◽  
Caroline Monaco Moreira ◽  
...  
Keyword(s):  
Rare Diseases ◽  
Segregation Analysis ◽  
Autosomal Dominant ◽  
Rare Variants ◽  
De Novo ◽  
Molecular Data ◽  
Autosomal Dominant Inheritance ◽  
Dominant Inheritance ◽  
Pathogenic Variants ◽  
Genomic Studies

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.

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

2021 ◽  
Author(s):  
Caio Robledo D' Angioli Costa Quaio ◽  
Jose Ricardo Magliocco Ceroni ◽  
Murilo Castro Cervato ◽  
Helena Strelow Thurow ◽  
Caroline Monaco Moreira ◽  
...  
Keyword(s):  
Segregation Analysis ◽  
Autosomal Dominant ◽  
Rare Variants ◽  
De Novo ◽  
Molecular Data ◽  
Autosomal Dominant Inheritance ◽  
Dominant Inheritance ◽  
Pathogenic Variants ◽  
Genomic Studies ◽  
Pattern Determination

Abstract 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.

scholarly journals Effective variant filtering and expected candidate variant yield in studies of rare human disease

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Brent S. Pedersen ◽  
Joe M. Brown ◽  
Harriet Dashnow ◽  
Amelia D. Wallace ◽  
Matt Velinder ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Rare Disease ◽  
Genome Sequencing ◽  
Autosomal Dominant ◽  
De Novo ◽  
Autosomal Dominant Inheritance ◽  
Compound Heterozygous ◽  
Whole Genome ◽  
Dominant Inheritance ◽  
Family Based

AbstractIn studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence variants vary from study to study. In an effort to establish recommendations for rare disease research, we explore effective guidelines for variant (SNP and INDEL) filtering and report the expected number of candidates for de novo dominant, recessive, and autosomal dominant modes of inheritance. We derived these guidelines using two large family-based cohorts that underwent whole-genome sequencing, as well as two family cohorts with whole-exome sequencing. The filters are applied to common attributes, including genotype-quality, sequencing depth, allele balance, and population allele frequency. The resulting guidelines yield ~10 candidate SNP and INDEL variants per exome, and 18 per genome for recessive and de novo dominant modes of inheritance, with substantially more candidates for autosomal dominant inheritance. For family-based, whole-genome sequencing studies, this number includes an average of three de novo, ten compound heterozygous, one autosomal recessive, four X-linked variants, and roughly 100 candidate variants following autosomal dominant inheritance. The slivar software we developed to establish and rapidly apply these filters to VCF files is available at https://github.com/brentp/slivar under an MIT license, and includes documentation and recommendations for best practices for rare disease analysis.

scholarly journals Expanding the Phenotypic Spectrum and Variability of Endocrine Abnormalities Associated With TUBB3 E410K Syndrome

2015 ◽  
Vol 100 (3) ◽  
pp. E473-E477 ◽  
Author(s):  
Ravikumar Balasubramanian ◽  
Sheena Chew ◽  
Sarah E. MacKinnon ◽  
Peter B. Kang ◽  
Caroline Andrews ◽  
...  
Keyword(s):  
Clinical Evaluation ◽  
Autosomal Dominant ◽  
De Novo ◽  
Hypogonadotropic Hypogonadism ◽  
Academic Medical Center ◽  
Autosomal Dominant Inheritance ◽  
Dominant Inheritance ◽  
Facial Weakness ◽  
Molecular Features ◽  
Social Disabilities

Context: A heterozygous de novo c.1228G>A mutation (E410K) in the TUBB3 gene encoding the neuronal-specific β-tubulin isotype 3 (TUBB3) causes the TUBB3 E410K syndrome characterized by congenital fibrosis of the extraocular muscles (CFEOM), facial weakness, intellectual and social disabilities, and Kallmann syndrome (anosmia with hypogonadotropic hypogonadism). All TUBB3 E410K subjects reported to date are sporadic cases. Objective: This study aimed to report the clinical, genetic, and molecular features of a familial presentation of the TUBB3 E410K syndrome. Design: Case report of a mother and three affected children with clinical features of the TUBB3 E410K syndrome. Setting: Academic Medical Center. Main Outcome Measures: Genetic analysis of the TUBB3 gene and clinical evaluation of endocrine and nonendocrine phenotypes. Results: A de novo TUBB3 c.1228G>A mutation arose in a female proband who displayed CFEOM, facial weakness, intellectual and social disabilities, and anosmia. However, she underwent normal sexual development at puberty and had three spontaneous pregnancies with subsequent autosomal-dominant inheritance of the mutation by her three boys. All sons displayed nonendocrine features of the TUBB3 E410K syndrome similar to their mother but, in addition, had variable features suggestive of additional endocrine abnormalities. Conclusions: This first report of an autosomal-dominant inheritance of the TUBB3 c.1228G>A mutation in a family provides new insights into the spectrum and variability of endocrine phenotypes associated with the TUBB3 E410K syndrome. These observations emphasize the need for appropriate clinical evaluation and complicate genetic counseling of patients and families with this syndrome.

Genomic features of lung cancer patients harboring germline mutations associated with hereditary cancer syndromes.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e20511-e20511
Author(s):  
Jian Sun ◽  
Weiran Wang ◽  
Danhua Wang ◽  
Hongling Yuan ◽  
Tonghui Ma
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Autosomal Recessive ◽  
Autosomal Dominant ◽  
Autosomal Recessive Inheritance ◽  
Germline Mutations ◽  
Autosomal Dominant Inheritance ◽  
Recessive Inheritance ◽  
Dominant Inheritance ◽  
Lung Cancer Patients

e20511 Background: Smoking and air pollution are the major causes of lung cancer; however, numerous studies have demonstrated that genetic factors also contribute to the development of lung cancer. Here, we reported an analysis of genomic features in 65 lung cancer patients with autosomal-dominant or autosomal-recessive inheritance of germline mutations. Methods: We retrospectively reviewed next-generation sequencing data of 26,904 lung cancer patients in a Chinese cohort. The germline mutation patterns, as well as the co-occurrence with somatic driver mutations were analyzed. Results: A total of 65 (0.24%) patients with heterozygous germline mutations associated with hereditary cancer syndromes were detected, including 27 (0.10%) patients with autosomal-dominant inheritance (BRCA1, BRCA2, RET and TP53) and 38 (0.14%) patients with autosomal-recessive inheritance (ATM, BLM, FANCA, FANCG, MUTYH, NBN, RECQL4 and WRN). Comparing to patients with autosomal-dominant inheritance (Age 56±17.8), patients with autosomal-recessive inheritance (Age 65±11.7, P = 0.009) were older, and there is no gender difference. Additionally, 66.7% (18/27) of patients with autosomal-dominant inheritance were identified co-mutated actionable variations, such as 12 patients harboring mutations in exon 18–21 of EGFR, 2 patients harboring ERBB2 exon 20 insertions, 3 patients harboring mutations in exon 2 of KRAS and 1 patient harboring EML4-ALK fusion. The coexistence of germline autosomal-dominant mutations and somatic driver mutations indicated that germline mutations have weak impact on lung cancer. Simultaneously, 52.6% (20/38) of patients with autosomal-recessive inheritance were identified co-mutated actionable variations, such as 15 EGFR+ patients, 2 ERBB2+ patients and 3 KRAS+ patients. And there was no significant difference in population frequency of co-mutated actionable variations between the two groups. Conclusions: In summary, studies on germline mutations of lung cancer patients may help to elucidate the etiology and mechanism of lung cancer, and may help for early detection and diagnosis, targeted therapy and improved prevention strategies.

Familial Spontaneous Pneumothorax

PEDIATRICS ◽  
1979 ◽  
Vol 64 (2) ◽  
pp. 172-175
Author(s):  
William G. Wilson ◽  
Arthur S. Aylsworth
Keyword(s):  
Statistical Analysis ◽  
Spontaneous Pneumothorax ◽  
Autosomal Dominant ◽  
Autosomal Dominant Inheritance ◽  
Familial Occurrence ◽  
Review Of The Literature ◽  
Dominant Inheritance ◽  
Pedigree Data ◽  
Fathers And Sons ◽  
Male To Female

A family is described in which four persons in three generations suffered spontaneous pneumothoraces: a newborn, an infant, an adolescent, and an adult. Review of the literature reveals 61 reports of familial spontaneous pneumothorax in 22 families. The ratio of male to female cases is approximately 1.8. Affected parents and affected children (including affected fathers and sons) are seen in ten families, while affected siblings with unaffected parents are noted in 13 families. Consanguinity has not been reported. Although autosomal dominant inheritance has been suggested as an explanation of familial spontaneous pneumothorax, available pedigree data are not adequate for statistical analysis. Physicians should be aware of the familial occurrence of spontaneous pneumothorax so that members of such families may be appropriately managed when problems arise.

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