Parental Segregation Research Articles

Mrc1 regulates parental histone segregation and heterochromatin inheritance

Chromatin-based epigenetic memory relies on the symmetric distribution of parental histones to newly synthesized daughter DNA strands, aided by histone chaperones within the DNA replication machinery. However, the mechanism of parental histone transfer remains elusive. Here, we reveal that in fission yeast, the replisome protein Mrc1 plays a crucial role in promoting the transfer of parental histone H3-H4 to the lagging strand, ensuring proper heterochromatin inheritance. In addition, Mrc1 facilitates the interaction between Mcm2 and DNA polymerase alpha, two histone-binding proteins critical for parental histone transfer. Furthermore, Mrc1's involvement in parental histone transfer and epigenetic inheritance is independent of its known functions in DNA replication checkpoint activation and replisome speed control. Instead, Mrc1 interacts with Mcm2 outside of its histone-binding region, creating a physical barrier to separate parental histone transfer pathways. These findings unveil Mrc1 as a key player within the replisome, coordinating parental histone segregation to regulate epigenetic inheritance.

Implementation of long-read sequencing for routine molecular diagnosis of familial mediterranean fever

BackgroundLong-read sequencing technology, widely used in research, is proving useful in clinical diagnosis, especially for infectious diseases. Despite recent advances, it hasn't been routinely applied to constitutional human diseases. Long-read sequencing detects intronic variants and phases variants, crucial for identifying recessive diseases. MethodsWe integrated long-read sequencing into the clinical diagnostic workflow for the MEFV gene, responsible for familial Mediterranean fever (FMF), using a Nanopore-based workflow. This involved long-range PCR amplification, native barcoding kit library preparation, GridION sequencing, and in-house bioinformatics. We compared this new workflow against our validated method using 39 patient samples and 3 samples from an external quality assessment scheme to ensure compliance with ISO15189 standards. ResultsOur evaluation demonstrated excellent performance, meeting ISO15189 requirements for reproducibility, repeatability, sensitivity, and specificity. Since October 2022, 150 patient samples were successfully analyzed with no failures. Among these samples, we identified 13 heterozygous carriers of likely pathogenic (LP) or pathogenic (P) variants, 1 patient with a homozygous LP/P variant in MEFV, and 4 patients with compound heterozygous variants. ConclusionThis study represents the first integration of long-read sequencing for FMF clinical diagnosis, achieving 100 % sensitivity and specificity. Our findings highlight its potential to identify pathogenic variants without parental segregation analysis, offering faster, cost-effective, and accurate clinical diagnosis. This successful implementation lays the groundwork for future applications in other constitutional human diseases, advancing precision medicine.

In Brassica rapa meiotic recombination; chromosome axis remodeling is critical

The primary mechanism by which breeders generate biodiversity is meiotic recombination, which permits genetic rearrangement at every generation. It facilitates the accumulation of advantageous alleles and eliminates harmful mutations. With the development of one to very rarely more than three crossovers that are not randomly distributed, this mechanism is highly regulated. To ensure correct parental chromosomal segregation and the creation of unique allelic combinations, meiotic recombination is essential. Finding the variables affecting the rate and distribution of meiotic crossings (COs) is crucial because this process is strictly regulated, especially for plant breeding initiatives. Nevertheless, few high-resolution recombination maps exist for most crops, including the Brassica genus, and little is known regarding sex differences and intraspecific variation. Here, using progenies of cross populations from the crossed F1s population, we reveal fine-scale resolution recombination landscapes for two female and one male cross in Brassica rapa. Parents are from very different lines, which stands for higher quality and yield.

Accurate parent-of-origin variant assignment for multiple hereditary cancer syndromes using proband-only blood sample analysis.

10516 Background: Predicting which side of the family a germline variant comes from is a critical gap in current clinical practice, vital for risk management, variant curation, and cascade genetic testing. Assignment of any autosomal variant to either parent with 99% accuracy is now possible with only a blood sample from the proband. Parent-of-Origin-Aware genomic analysis (POAga) is achieved by combining methylation and sequence data from Oxford Nanopore long-read sequencing with chromosome-length haplotypes generated from Strand-seq to infer parent of origin of any variant along the length of a chromosome, due to accurate phasing of imprinted differentially methylated regions that occur on each autosome. We sought to validate POAga in common, high penetrant hereditary cancer conditions such as hereditary breast and ovarian cancer (HBOC) and Lynch syndrome, rarer syndromes with parent-of-origin-effects and other genes predisposing to breast cancer and gastrointestinal malignancies that are associated with genes across multiple chromosomes. Methods: Blood samples from carriers of pathogenic variants in ATM, BRCA1, BRCA2, CDH1, MLH1, MSH2, MSH6, PMS2, EPCAM, PALB2, SDHD and SDHAF2, with known parental segregation, are currently being ascertained to determine the analytic validity of POAga in real world samples of differing age, sex, ethnicity, and cancer status. Samples are undergoing whole genome analysis by long and short read sequencing. Parent-of-origin of the pathogenic or likely pathogenic variant or variant of uncertain significance is predicted according to previously described methods (Akbari V, Hanlon VCT, et al. Cell Genom. 2022 Dec 21;3(1):100233.) under an REB approved protocol. Results: To date, analysis is complete for 100 individuals with a total of 107 rare or pathogenic germline variants with known or presumed parental segregation. Germline variants are in SDHD (n = 18), BRCA2 (n = 17), BRCA1 (n = 14), MLH1 (n = 10), PALB2 (n = 9), PMS2 (n = 8), MSH2 (n = 9), MSH6 (n = 7), ATM (n = 5), CDH1 (n = 5), SDHAF2 (n = 1), DICER1 (n = 1), MUTYH (n = 1), RET (n = 1), and EPCAM (n = 1). Of variants able to be assigned a parent-of-origin (n = 104 of 107, 97%), there was complete concordance between the predicted parent-of-origin and known clinical segregation (n = 104, 100%). Conclusions: Results to date support the ability of POAga to accurately infer parent-of-origin of rare or pathogenic variants with known parental segregation using only a blood sample from carriers of diverse hereditary cancer syndromes. Ongoing validation of POAga will continue to test its feasibility in real-world samples and inform its path towards clinically translation. Parent-of-Origin-Aware genomic analysis is a powerful technology that could improve our understanding of hereditary cancer syndromes and transform our ability to conduct genetic cancer risk assessments for patients and families.

Coordination of histone chaperones for parental histone segregation and epigenetic inheritance.

Chromatin-based epigenetic memory relies on the accurate distribution of parental histone H3-H4 tetramers to newly replicated DNA strands. Mcm2, a subunit of the replicative helicase, and Dpb3/4, subunits of DNA polymerase ε, govern parental histone H3-H4 deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. Here, using fission yeast heterochromatin inheritance systems that eliminate interference from initiation pathways, we show that a Mcm2 histone binding mutation severely disrupts heterochromatin inheritance, while mutations in Dpb3/4 cause only moderate defects. Surprisingly, simultaneous mutations of Mcm2 and Dpb3/4 stabilize heterochromatin inheritance. eSPAN (enrichment and sequencing of protein-associated nascent DNA) analyses confirmed the conservation of Mcm2 and Dpb3/4 functions in parental histone H3-H4 segregation, with their combined absence showing a more symmetric distribution of parental histone H3-H4 than either single mutation alone. Furthermore, the FACT histone chaperone regulates parental histone transfer to both strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone H3-H4 density and faithful heterochromatin inheritance. These results underscore the importance of both symmetric distribution of parental histones and their density at daughter strands for epigenetic inheritance and unveil distinctive properties of parental histone chaperones during DNA replication.

Five Novel Hemizygous Variants in the PGK1 Gene Associated with Neurological Dysfunction and Mild Hemolytic Anemia in Five Indian Patients

Introduction Phosphoglycerate kinase (ATP: 3-phosphoglycerate 1-phosphotransferase; EC 2.7.2.3; PGK) is the crucial enzyme of the glycolytic pathway, catalyzing1, 3 bis-phosphoglycerate to 3-Phosphoglycerate, generating one molecule of ATP [1]. PGK enzyme is encoded by the PGK1 gene located at Xq13.3, measures 23kb in size, and spans into 11 exons. PGK deficiency is an X-linked disorder associated with a very rare cause of hereditary non-spherocytic hemolytic anemia (HNSHA). PGK1 gene is ubiquitously expressed but the patients exhibit three major symptoms -1) haemolytic anemia 2) myopathy (rhabdomyolysis), 3) mental retardation and various neurological manifestations[1]. The severity of symptoms varies among patients with PGK deficiency. PGK deficiency is reported worldwide, although to our knowledge no case with Indian ancestry has been reported. Method Genomic DNA was extracted from the EDTA blood sample and processed for targeted Next Generation Sequencing (t-NGS) as per the manufacturer's protocol. The t-NGS panel broadly consists of 80 genes of the spectrum of the disorder including congenital hemolytic anemia, bone marrow failure disorders, and iron deficiency anemia. The libraries were sequenced to >80-100X mean coverage on the Illumina sequencing platform. The variants were classified based on ACMG guidelines. The impact of non-synonymous variations was estimated using PolyPhen-2, SIFT, MutationTaster2, CADD Phred, and Mutpred2. In silico effect of the variant was studied by PyMol. Latter the enzyme deficiency was confirmed by standard protocol and parental segregation analysis was performed. Relative quantification (qPCR) was evaluated based on the comparative CT method ( 2 − ΔΔCT). Result We report five male children of <4 years of age with PGK deficiency from Indian origin. Clinically, all of them manifest global development delay and no speech. Autism spectrum disorder is observed in two of the cases, incidence of seizure and convulsion are present in two cases. None except one, presented with haemolytic anaemia and was given one transfusion post an episode of seizure at the age of 2 years. Additionally, a family history of haemolytic anemia with developmental delay and seizure was present in only one case although the patient himself required no transfusion requirement to date. All the patients are routinely followed up for any evidence of a haemolytic crisis, transfusion requirement, or any other clinical symptoms. Detailed phenotypes of all the patients are listed in Table 1. t-NGS revealed five novel hemizygous variants in the PGK1 gene - p. Cys50Trp, p. Gly137Trp, p. Val140Ile, p. Asp159Asn, and p. Arg330Trp. These variants have not been reported in the literature or available databases. DNA Sanger sequencing confirmed the heterozygous state in the mothers. In silico tools confirmed the pathogenicity of the variants. The PGK enzymatic activity was markedly reduced. The PGK1 transcript levels were reduced to 60% in patients as compared to the healthy controls. Discussion To date, only 34 mutations are known to be associated with PGK enzyme deficiency. Amongst them, 50% of variants exhibit symptoms of anaemia whereas the remaining show neurological and /or myopathy. Figure 1 illustrates all 39 mutations reported with PGK deficiency. Only four mutations p.E120K, p.G158R, p.A354P, and p.I371K are known to exhibit all three categories of symptom (PGK-anaemia-neurological-myopathy)[2]. Conclusion NGS allows for the identification of novel genetic variants that may contribute to the development of rare disorders, expanding our knowledge of their underlying mechanisms. This advanced technology also enables researchers to analyze multiple genes simultaneously, increasing the efficiency and speed of diagnosis in unexplained cases of HNSHA.

PP2A-B55SUR-6 promotes nuclear envelope breakdown in C. elegans embryos

Nuclear envelope (NE) disassembly during mitosis is critical to ensure faithful segregation of the genetic material. NE disassembly is a phosphorylation-dependent process wherein mitotic kinases hyper-phosphorylate lamina and nucleoporins to initiate nuclear envelope breakdown (NEBD). In this study, we uncover an unexpected role of the PP2A phosphatase B55SUR-6 in NEBD during the first embryonic division of Caenorhabditis elegans embryo. B55SUR-6 depletion delays NE permeabilization and stabilizes lamina and nucleoporins. As a result, the merging of parental genomes and chromosome segregation is impaired. NEBD defect upon B55SUR-6 depletion is not due to delayed mitotic onset or mislocalization of mitotic kinases. Importantly, we demonstrate that microtubule-dependent mechanical forces synergize with B55SUR-6 forefficient NEBD. Finally, our data suggest that the lamin LMN-1 is likely a bona fide target of PP2A-B55SUR-6. These findings establish a model highlighting biochemical crosstalk between kinases, PP2A-B55SUR-6 phosphatase, and microtubule-generated mechanical forces in timely NE dissolution.

Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: evidence supporting whole exome sequencing as first tier test

BackgroundAutism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic architecture of ASD in India. This study aimed to identify the genetic architecture of ASD in India and to assess the use of whole exome sequencing (WES) as a first-tier test instead of chromosomal microarray (CMA) for genetic diagnosis.MethodsBetween 2020 and 2022, 101 patient-parent trios of Indian origin diagnosed with ASD according to the Diagnostic and Statistical Manual, 5th edition, were recruited. All probands underwent a sequential genetic testing pathway consisting of karyotyping, Fragile-X testing (in male probands only), CMA and WES. Candidate variant validation and parental segregation analysis was performed using orthogonal methods.ResultsOf 101 trios, no probands were identified with a gross chromosomal anomaly or Fragile-X. Three (2.9%) and 30 (29.7%) trios received a confirmed genetic diagnosis from CMA and WES, respectively. Amongst diagnosis from WES, SNVs were detected in 27 cases (90%) and CNVs in 3 cases (10%), including the 3 CNVs detected from CMA. Segregation analysis showed 66.6% (n = 3 for CNVs and n = 17 for SNVs) and 16.6% (n = 5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. MECP2 gene was the most recurrently mutated gene (n = 6; 20%) in the present cohort. Majority of the affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling.ConclusionsOur study suggests de novo variants as a major cause of ASD in the Indian population, with Rett syndrome as the most commonly detected disorder. Furthermore, we provide evidence of a significant difference in the diagnostic yield between CMA (3%) and WES (30%) which supports the implementation of WES as a first-tier test for genetic diagnosis of ASD in India.

Mutation in Methionyl-tRNA Synthetase 1 Causing Pulmonary Alveolar Proteinosis

Background: A chronic history of exertional dyspnea, dry cough, and fatigue, associated with reticulonodular ground-glass opacity indicates an underlying interstitial lung disease (ILD). Pulmonary alveolar proteinosis (PAP) is a rare cause of ILD, in which there is abnormal accumulation of surfactant material in alveoli, thereby impairing gaseous exchange. In children, PAP is usually due to genetic mutations. We report a child with PAP due to mutation in methionyl-transfer RNA synthetase 1 (MARS) gene. Clinical Description: An 8-year-old boy presented with persistent dry cough, and exercise-induced breathlessness for 2 years of age, associated with failure to gain weight. He had multiple exacerbations in the past, requiring common symptomatic treatment, but with minimal improvement. On presentation to us, the child had tachypnea, hypoxia (oxygen saturation [SpO2]: 85%), and Grade 2 clubbing, with bilateral fine crepitation in bilateral lung fields. Management and Outcome: The child was stabilized by providing oxygen via high-flow nasal cannula. Blood investigations were largely normal. His chest X-ray and computerized tomography (CT) of the chest were suggestive of childhood ILD. A lung biopsy revealed periodic acid–Schiff-positive eosinophilic granular material in the alveolar spaces without any fibrosis, suggesting a diagnosis of PAP. Next-generation sequencing revealed a compound heterozygous mutation of the MARS1 gene resulting in PAP. Parental segregation analysis showed each one to be a carrier of one of the genes. Therapeutic whole-lung lavage (WLL) was carried out, following which symptoms improved markedly. SpO2 increased and the child was able to be weaned off oxygen and discharged. Three years, postdischarge, the child is asymptomatic and thriving well. Conclusions: PAP may be a cause of ILD in a child. Although the etiology can be ascertained by high-resolution CT of the chest and bronchoalveolar lavage, further genetic analysis should also be undertaken in children to identify the exact defect. WLL can provide a good outcome in children with PAP due to MARS mutation.

Implementing a germline testing program using fingernail specimens for patients with hematologic malignancies and initial clinical findings.

10632 Background: About 5-20% of hematologic malignancies (HM) occur in the setting of a genetic cancer predisposition syndrome. Additionally, overt constitutional syndromes involving multiple systems may also predispose to HM. The spectrum of cancer predisposition in patients with HM has been limited partially due to the difficulty of germline sample ascertainment from patients with liquid tumors as skin biopsies and fibroblast cultures are often required for testing. Methods: Hematologic malignancy patients enrolled in Memorial Sloan Kettering Cancer Center’s institutional 12-245 study who were having somatic testing performed on their tumor were given the option to consent to germline testing using fingernail specimens. The validated germline assay using nails as a sample type was approved as a clinical test by the New York State Department of Health. Samples were analyzed using a custom panel consisting of 82 cancer predisposition genes. Single nucleotides, insertions deletions, and copy number variants were detected using our analytic pipeline and analyzed according to ACMG criteria for pathogenicity. Only pathogenic and likely pathogenic germline variants (gPV) were returned. Results: Among 86 HM patients (acute myeloid leukemia, n = 19; myelodysplastic syndrome, n = 16; acute B lymphoblastic leukemia, n = 9; acute T-cell leukemia, n = 4; mixed phenotypic acute leukemia, n = 1; chronic lymphocytic leukemia, n = 7; hairy cell leukemia, n = 1; chronic myeloid leukemia, n = 4; chronic myelomonocytic leukemia, n = 1, non-Hodgkin lymphoma, n = 12; Hodgkin lymphoma, n = 8; and multiple myeloma, n = 4), gPV were detected in 16 % (14/86). Heterozygous gPV identified in high/moderate penetrant genes included 2 BRCA1, 2 ATM, 1 PALB2, and 3 CHEK2. Monoallelic carriers for homozygous disease included 2 MUTYH and 1 MSH3. Biallelic gPV were identified in 3 patients (1 FANCA, 1 ATM, 1 MSH6); the patients with Fanconi anemia (age 25) manifesting with MDS and constitutional mismatch repair deficiency (age 13) presenting with T-cell lymphoblastic lymphoma had not been previously diagnosed with these conditions and did not have obvious clinical features outside of their cancer diagnosis. In all 3 patients, identification of an autosomal recessive syndrome impacted therapeutic planning. Conclusions: Our study demonstrates the feasibility of utilizing nails, a non-contaminated germline sample source, for HM predisposition with a significant proportion of pediatric and adult HM patients identified to harbor gPV in a cancer predisposition gene. Autosomal recessive diseases should be considered not only in pediatrics but also adult patients and requires confirmation of allele segregation in parents. Our data also demonstrate the importance of gPV in HM for therapeutic planning.

Proband only exome sequencing in 403 Indian children with neurodevelopmental disorders: Diagnostic yield, utility and challenges in a resource-limited setting.

Whole exome sequencing is recommended as the first tier test for neurodevelopmental disorders (NDDs) with trio being an ideal option for the detection of de novo variants. Cost constraints have led to adoption of sequential testing i.e. proband-only whole exome followed by targeted testing of parents. The reported diagnostic yield for proband exome approach ranges between 31 and 53%. Typically, these study designs have aptly incorporated targeted parental segregation before concluding a genetic diagnosis to be confirmed. The reported estimates however do not accurately reflect the yield of proband only standalone whole -exome, a question commonly posed to the referring clinician in self pay medical systems like India. To assess the utility of standalone proband exome (without follow up targeted parental testing), we retrospectively evaluated 403 cases of neurodevelopmental disorders referred for proband-only whole exome sequencing at Neuberg Centre for Genomic Medicine (NCGM), Ahmedabad during the period of January 2019 and December 2021. A diagnosis was considered confirmed only upon the detection of Pathogenic/Likely Pathogenic variants in concordance with patient's phenotype as well as established inheritance pattern. Targeted parental/familial segregation analysis was recommended as a follow up test where applicable. The diagnostic yield of the proband-only standalone whole exome was 31.5%. Only 20 families submitted samples for follow up targeted testing, and a genetic diagnosis was confirmed in twelve cases increasing the yield to 34.5%. To understand factors leading to poor uptake of sequential parental testing, we focused on cases where an ultra-rare variant was detected in hitherto described de novo dominant neurodevelopmental disorder. A total of 40 novel variants in genes associated with de novo autosomal dominant disorders could not be reclassified as parental segregation was denied. Semi-structured telephonic interviews were conducted upon informed consent to comprehend reasons for denial. Major factors influencing decision making included lack of definitive cure in the detected disorders; especially when couples not planning further conception and financial constraints to fund further targeted testing. Our study thus depicts the utility and challenges of proband-only exome approach and highlights the need for larger studies to understand factors influencing decision making in sequential testing.

Dental Phenotype with Minor Ectodermal Symptoms Suggestive of WNT10A Deficiency

Ectodermal dysplasias (EDs) represent a heterogeneous group of genetic disorders characterized by the abnormal development of ectodermal-derived tissues. They include the involvement of the hair, nails, skin, sweat glands, and teeth. Pathogenic variants in EDA1 (Xq12-13.1; OMIM*300451), EDAR (2q11-q13; OMIM*604095), EDARADD (1q42-q43, OMIM*606603), and WNT10A (2q35; OMIM*606268) genes are responsible for most EDs. Bi-allelic pathogenic variants of WNT10A have been associated with autosomal recessive forms of ED, as well as non-syndromic tooth agenesis (NSTA). The potential phenotypic impact of associated modifier mutations in other ectodysplasin pathway genes has also been pointed out. We present on an 11-year-old Chinese boy with oligodontia, with conical-shaped teeth as the main phenotype, and other very mild ED signs. The genetic study identified the pathogenic variants WNT10A (NM_025216.3): c.310C > T; p. (Arg104Cys) and c.742C > T; p. (Arg248Ter) in compound heterozygosis, confirmed by parental segregation. In addition, the patient had the polymorphism EDAR (NM_022336.4): c.1109T > C, p. (Val370Ala) in homozygosis, named EDAR370. A prominent dental phenotype with minor ectodermal symptoms is very suggestive of WNT10A mutations. In this case, the EDAR370A allele might also attenuate the severity of other ED signs.

P566: Importance Of parental segregation studies and its role in variant classification

P566: Importance Of parental segregation studies and its role in variant classification

Parental genomes segregate into distinct blastomeres during multipolar zygotic divisions leading to mixoploid and chimeric blastocysts

BackgroundDuring normal zygotic division, two haploid parental genomes replicate, unite and segregate into two biparental diploid blastomeres.ResultsContrary to this fundamental biological tenet, we demonstrate here that parental genomes can segregate to distinct blastomeres during the zygotic division resulting in haploid or uniparental diploid and polyploid cells, a phenomenon coined heterogoneic division. By mapping the genomic landscape of 82 blastomeres from 25 bovine zygotes, we show that multipolar zygotic division is a tell-tale of whole-genome segregation errors. Based on the haplotypes and live-imaging of zygotic divisions, we demonstrate that various combinations of androgenetic, gynogenetic, diploid, and polyploid blastomeres arise via distinct parental genome segregation errors including the formation of additional paternal, private parental, or tripolar spindles, or by extrusion of paternal genomes. Hence, we provide evidence that private parental spindles, if failing to congress before anaphase, can lead to whole-genome segregation errors. In addition, anuclear blastomeres are common, indicating that cytokinesis can be uncoupled from karyokinesis. Dissociation of blastocyst-stage embryos further demonstrates that whole-genome segregation errors might lead to mixoploid or chimeric development in both human and cow. Yet, following multipolar zygotic division, fewer embryos reach the blastocyst stage and diploidization occurs frequently indicating that alternatively, blastomeres with genome-wide errors resulting from whole-genome segregation errors can be selected against or contribute to embryonic arrest.ConclusionsHeterogoneic zygotic division provides an overarching paradigm for the development of mixoploid and chimeric individuals and moles and can be an important cause of embryonic and fetal arrest following natural conception or IVF.

Exome sequencing for patients with developmental and epileptic encephalopathies in clinical practice.

To assess the clinical utility of exome sequencing for patients with developmental and epileptic encephalopathies (DEEs). Over 2 years, patients with DEEs were recruited for singleton exome sequencing. Parental segregation was performed where indicated. Of the 103 patients recruited (54 males, 49 females; aged 2 weeks-17 years), the genetic aetiology was identified in 36 out of 103 (35%) with management implications in 13 out of 36. Exome sequencing revealed pathogenic or likely pathogenic variants in 30 out of 103 (29%) patients, variants of unknown significance in 39 out of 103 (38%), and 34 out of 103 (33%) were negative on exome analysis. After the description of new genetic diseases, a molecular diagnosis was subsequently made for six patients or through newly available high-density chromosomal microarray testing. We demonstrate the utility of exome sequencing in routine clinical care of children with DEEs. We highlight that molecular diagnosis often leads to changes in management and informs accurate prognostic and reproductive counselling. Our findings reinforce the need for ongoing analysis of genomic data to identify the aetiology in patients in whom the cause is unknown. The implementation of genomic testing in the care of children with DEEs should become routine in clinical practice. The cause was identified in 35% of patients with developmental and epileptic encephalopathies. KCNQ2, CDKL5, SCN1A, and STXBP1 were the most frequently identified genes. Reanalysis of genomic data found the cause in an additional six patients. Genetic aetiology was identified in 41% of children with seizure onset under 2 years, compared to 18% with older onset. Finding the molecular cause led to management changes in 36% of patients with DEEs.

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 and 211 as likely benign. 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.

EP404: Evidence supporting the pathogenicity of the NADSYN1 c.1717G>A (p.Ala573Thr) variant in individuals referred for clinical testing

Vertebral, cardiac, renal, and limb defects syndrome 3 (VCRL3; OMIM #618845) is an autosomal recessive multiple congenital anomaly syndrome caused by pathogenic variants in the NADSYN1 gene. NADSYN1 encodes a nicotinamide adenine dinucleotide (NAD) synthetase that is part of the de novo NAD synthesis pathway. Other genes involved in this pathway include HAAO and KYNU. Genetic variants in any of these genes result in reduced de novo NAD synthesis and cause congenital anomalies of the heart, kidney, and vertebrae. Of note, presence of these three features is also considered clinical evidence for vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, renal anomalies, and limb abnormalities (VACTERL) association, which is often a diagnosis of exclusion (ie, other genetic conditions with overlapping features must be ruled out before assigning this diagnosis). The recommended approach for genetic testing in possible VACTERL patients is to either pursue a comprehensive testing option, such as exome or genome sequencing, or a panel approach with the most likely candidates. The NADSYN1 gene is included on a VACTERL Association and Related Disorders panel and several patients were noted to be homozygous for the NADSYN1 c.1717G>A (p.Ala573Thr) variant, thus providing additional evidence for both the pathogenicity and high carrier frequency of this change. To date, we have identified five patients who are homozygous for the NADSYN1 (NM_018161.4) c.1717G>A (p.Ala573Thr) variant. One patient was identified through targeted testing, one through testing with the VACTERL Association and Related Disorders panel, and three through exome sequencing. The first four cases were from pregnancies evaluated for the differential diagnosis of VACTERL association via panel testing or exome sequencing. All four fetuses were reported to have cardiac malformation and segmental vertebral anomalies. Parental data was available for three of the four fetuses, and all parents tested were heterozygous for the NADSYN1 c.1717G>A (p.Ala573Thr) variant. All cases denied consanguinity. In contrast to the severe and early onset features of the other four patients identified, the targeted testing case was an adult patient who previously had the NADSYN1 c.1717G>A variant identified in a research study. This individual was noted to have cardiac defects, vertebral defects, and short stature. This variant is relatively common in non-Finnish Europeans with an allele frequency of 0.15% in the gnomAD v2 dataset. Five patients from four families with VCRL3 have been described in the literature. Of these patients, three had the c.1717G>A variant: two homozygous siblings and one compound heterozygote with a loss of function variant on the opposite allele. Parental sequencing data confirmed the biallelic variants in all reported patients. In addition, yeast model functional studies performed by Szot and colleagues demonstrated that the p.Ala573Thr change diminished NAD synthetase activity and reduced yeast viability, consistent with a loss of function mechanism. Taken together, although the NADSYN1 c.1717G>A (p.Ala573Thr) has a relatively high minor allele frequency, there is sufficient evidence for this variant to be classified as pathogenic using ACMG/AMP variant classifications and internal variant interpretation guidelines. The NADSYN1 c.1717G>A (p.Ala573Thr) variant should be interpreted as pathogenic given the 5 additional homozygous patients and parental segregation data presented here. Additionally, the diagnosis of VCRL3 in an adult patient suggests that although penetrance for NAD deficiency is complete, variable expressivity is observed and could be explained by other genetic or non-genetic factors modulating disease severity. Given the high population frequency of this variant, genetic testing for VACTERL association should always include evaluation of NADSYN1 to consider VCRL3 in the differential diagnosis.

High Incidence of COL4A Genetic Variants Among a Cohort of Children With Steroid-Resistant Nephrotic Syndrome From Eastern India

High Incidence of COL4A Genetic Variants Among a Cohort of Children With Steroid-Resistant Nephrotic Syndrome From Eastern India

Kleefstra syndrome: Recurrence in siblings due to a paternal mosaic mutation

Kleefstra syndrome (KS) is a rare autosomic dominant genetic disorder caused by euchromatic histone methyltransferase 1 (EHMT1) alterations. Patients mainly present with moderate to severe intellectual disability, a severe delay in/or absence of speech, autism spectrum disorder, childhood hypotonia, neuropsychiatric anomalies, and distinctive dysmorphic features. Here, we report the cases of a male and a female, two younger siblings of three, with asymptomatic parents. An EHMT1 new mutation was identified. Both presented with a typical core phenotype. Some specific features were noted, such as macrocephaly (previously reported) and enuresis (not yet described). Parental analysis identified the mutation in the mosaic state in the father. Reverse phenotyping enabled us to highlight the pauci phenotype features of inguinal hernia, azoospermia, and possible behavioral disorders. This allowed us to adapt his follow-up and genetic counseling for the family. Our three reported cases provide a new description of KS with an intragenic EHMT1 mutation, whereas in the literature most reported cases have EHMT1 deletions. Moreover, in the areas of next-generation sequencing and trio techniques with parental segregation, it is important to remain cautious about disregarding variants based on an autosomal recessive hypothesis.

P–207 Heterogoneic cell division proven to occur in bovine zygotes

Abstract Study question We hypothesize that the zygote can segregate parental genomes via a non-canonical pathway. We coined this heterogoneic cell division. Can we proof the existence of this new segregational pathway? Summary answer We confirmed the existence of this non-canonical segregation mechanism leading to mixoploidy and provide a catalogue of abnormal zygotic divisions. What is known already Embryos show a high degree of chromosomal instability leading to chromosomal mosaicism. Chromosomal aberrations affect the developmental potential. We developed haplarithmisis which determines the single-cell genome-wide haplotype and copy number and allows to deduce the parental and segregational origin. Analysis of cleavage-stage bovine embryos by haplarithmisis, discovered the presence of uniparental and biparental blastomere lineages in individual embryos. We hypothesized that whole genome segregations can occur via a non-canonical zygotic division, a process termed “heterogoneic” division. Abnormal zygotic division has been observed in bovine and human in vitro produced zygotes using time-lapse, but parental genome segregation has never been disclosed. Study design, size, duration We hypothesized that abnormal cytokinetics and spindle mechanics may underlie the segregation of parental genomes in a separate blastomere line. In vitro produced zygotes were monitored by time-lapse microscopy. Zygotes cleaving 3 or 4 cells were disaggregated, picked and analysed by haplarithmisis. Participants/materials, setting, methods Blastomeres from bovine in vitro produced zygotes cleaving directly into 3 or 4 blastomeres, identified by time-lapse monitoring, were tubed following zona removal and blastomere dissociation and whole-genome amplified. Samples were subsequently hybridized on Illumina Bovine HD BeadChip SNP arrays. Data was analyzed by haplarithmisis, using a the siCHILD-bovine algorithm, to infer the haplotypes and the copy number of the parental genomes. Blastomeres showing failed haplarithmisis plots were low-coverage whole-genome sequenced on a HiSeq4000 sequencer. Main results and the role of chance: We obtained 25 bovine embryos, comprising 82 blastomeres, derived from 12 families (12 cows and 2 bulls) that cleaved directly into 3 or 4 blastomeres. Sixteen, 7 and 2 out of 25 zygotes cleaved respectively in 3 cells, 4 cells and 3 cells and a fragment. In at least 20 embryos, more than one paternal haplotype was identified, showing that a polyspermic fertilization resulted in an abnormal division. All embryos contained a whole-genome abnormality in at least one blastomere, resulting in mixoploid (5), mixed diploid biparental and androgenetic (12), polyploid (4), mixed gynogenetic and androgenetic (2) and androgenetic (2) embryos. Twenty-one embryos had at least one blastomere containing a uniparental signature. Based on the blastomere haplotype profiles we classified the embryos in six segregation categories. In twelve blastomeres haplarithmisis failed. Massive parallel sequencing of the amplified DNA showed the presence of mitochondrial DNA, indicating the blastomere did not contain any genomic DNA. This observation confirms that heterogoneic cell division does occur via different non-canonical zygotic segregations, which result in a variety of chimeric and mixoploid embryos constitutions. Limitations, reasons for caution These findings apply to a small set of bovine in vitro produced abnormally cleaving embryos. Segregation patterns may be incomplete and their true in vitro and in vivo prevalence remains unknown. Based on the haplotypes the non-canonical divisions have been reconstructed. Those patterns can now be evaluated and tested. Wider implications of the findings: This study shows that heterogoneic cell division occurs. We hypothesize this non-canonical division occurs frequently in both in vitro and in vivo, not only in cattle but also in man and hypothesize that persistence of such cell lines might explain the development of androgenetic tumorous outgrowths and mosaic uniparental individuals. Trial registration number Not applicable