Implications For Genetic Counseling Research Articles

Characterization of D4Z4 alleles and assessment of de novo cases in Facioscapulohumeral dystrophy (FSHD) in a cohort of Italian families.

Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant disease, although 10%-30% of cases are sporadic. However, this percentage may include truly de novo patients (carrying a reduced D4Z4 allele that is not present in either of the parents) and patients with apparently sporadic disease resulting from mosaicism, non-penetrance, or complex genetic situations in either patients or parents. In this study, we characterized the D4Z4 Reduced Alleles (DRA) and evaluated the frequency of truly de novo cases in FSHD1 in a cohort of DNA samples received consecutively for FSHD-diagnostic from 100 Italian families. The D4Z4 testing revealed that 60 families reported a DRA compatible with FSHD1 (1-10 RU). The DRA co-segregated with the disease in most cases. Five families with truly de novo cases were identified, suggesting that this condition may be slightly lower (8%) than previously reported. In addition, D4Z4 characterization in the investigated families showed 4% of mosaic cases and 2% with translocations. This study further highlighted the importance of performing family studies for clarifying apparently sporadic FSHD cases, with significant implications for genetic counseling, diagnosis, clinical management, and procreative choices for patients and families.

Clinical Experience of Prenatal Chromosomal Microarray Analysis in 6159 Ultrasonically Abnormal Fetuses.

A single-center retrospective study of G-band karyotyping and chromosomal microarray analysis (CMA) for the invasive prenatal diagnosis of 6159 fetuses with ultrasound abnormalities was conducted. This study aimed to investigate the incidence rates of chromosomal abnormalities and pregnancy outcomes and postpartum clinical manifestations by long-term follow-up and to explore the correlation between different types of prenatal ultrasound abnormalities and pathogenic chromosomal abnormalities. The overall incidence of pathogenic chromosomal aberrations in fetuses with ultrasound abnormalities was 7.58% (467/6159), which comprised 41.7% (195/467) with chromosome number abnormalities, 57.6% (269/467) with pathogenic copy-number variations (pCNVs), and 0.64% (3/467) with uniparental disomy (UPD). In addition, 1.72% (106/6159) with likely pathogenic copy-number variations (lpCNVs) and 3.04% (187/6159) with variants of unknown significance (VOUS) were detected by CMA. Ultrasound abnormalities were categorized into structural anomalies and soft marker anomalies. The incidence rate of pathogenic and likely pathogenic chromosomal abnormalities was significantly higher among fetuses with structural anomalies than soft markers (11.13% vs 7.59%, p < 0.01). We retrospectively analyzed the prenatal genetic outcomes for a large cohort of fetuses with different types of ultrasound abnormalities. The present study showed that the chromosomal abnormality rate and clinical outcomes of fetuses with different types of ultrasound abnormalities varied greatly. Our data have important implications for prenatal genetic counseling for fetuses with different types of ultrasound abnormalities.

Phenotype-genotype discordance in patients with hypertrophic cardiomyopathy: clinical and echocardiographic correlates

Abstract Introduction Hypertrophic cardiomyopathy (HCMP) is a common genetic disorder characterized by asymmetric septal hypertrophy (ASH) on echocardiography. However, the diagnosis of HCMP can be challenging, as not all patients with ASH have a pathogenic genetic mutation. Purpose The aim of this study was to investigate the clinical and echocardiographic correlates of phenotype-genotype discordance in patients with HCMP feature in clinical field. Methods The study included 28 patients with an HCM phenotype confirmed by echocardiography with ASH. The patients underwent whole exome sequencing (WES) for genetic testing, were divided into two groups based on the presence (concordance group) or absence (discordance group) of a pathogenic mutation on WES. Echocardiographic parameters, including interventricular septum thickness at end-diastole (IVSd), interventricular septum thickness at end-systole (IVSs), posterior wall thickness at end-diastole (PWd), posterior wall thickness at end-systole (PWs), and global average strain (GAS), were compared between the two groups. Receiver operating characteristic (ROC) curve analysis was performed to identify the echocardiographic parameters that could predict genotype discordance. Results Only 11 out of 28 patients (39%) showed an HCM genotype result by WES. The discordance group (n=17) showed significantly higher PWd (p=0.001), PWs (p=0.005) and lower left ventricle mass (p=0.024) than the concordance group (n=11). The discordance group also showed a decreased tendency in GAS compared to the concordant group. In ROC curve analysis, PWd could reversely predict the phenotype-genotype concordance with a sensitivity of 81.8% and specificity of 71.4% (area under the curve=0.841, p=0.004). Conclusion The study suggests that there is a high discordance rate between phenotype and genotype in patients with HCM. Echocardiographic parameters, especially PWd and PWs, may be useful in predicting phenotype-genotype discordance. These findings have important implications for clinical management and genetic counseling in patients with suspected HCMP.

Expanding the genetic and clinical spectrum of osteogenesis imperfecta: identification of novel rare pathogenic variants in type I collagen-encoding genes.

Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous skeletal disorder. The majority of affected cases are attributed to autosomal dominant pathogenic variants (PVs) found in the COL1A1 and COL1A2 genes, which encode type I collagen. However, PVs in other genes involved in collagen posttranslational modification, processing, crosslinking, osteoblast differentiation, and bone mineralization have also been associated with OI. In this study, we present the results of next-generation sequencing (NGS) analysis using a custom panel of 11 genes known to be associated with OI. This clinical study enrolled a total of 10 patients, comprising 7 male and 3 female patients from 7 families, all from the Puglia Region in South Italy, providing a detailed overview of their age, gender, family history, OI type, and non-skeletal features. The genetic analysis revealed 5 PVs in the COL1A1 gene and 2 PVs in the COL1A2 gene. Importantly, three of these PVs have not been previously reported in the literature. These include two novel heterozygous frameshift PVs in COL1A1 (c.2890_2893del and c.3887del) and one novel heterozygous missense PV in COL1A2 (c.596G>T). The identification of these previously unreported PVs expands the variant spectrum of the COL1A1 and COL1A2 genes and may have implications for accurate diagnosis, genetic counselling, and potential therapeutic interventions in affected individuals and their families.

Whole exome sequencing revealed variants in four genes underlying X-linked intellectual disability in four Iranian families: novel deleterious variants and clinical features with the review of literature

Aim and ObjectiveIntellectual disability (ID) is a heterogeneous condition affecting brain development, function, and/or structure. The X-linked mode of inheritance of ID (X-linked intellectual disability; XLID) has a prevalence of 1 out of 600 to 1000 males. In the last decades, exome sequencing technology has revolutionized the process of disease-causing gene discovery in XLIDs. Nevertheless, so many of them still remain with unknown etiology. This study investigated four families with severe XLID to identify deleterious variants for possible diagnostics and prevention aims.MethodsNine male patients belonging to four pedigrees were included in this study. The patients were studied genetically for Fragile X syndrome, followed by whole exome sequencing and analysis of intellectual disability-related genes variants. Sanger sequencing, co-segregation analysis, structural modeling, and in silico analysis were done to verify the causative variants. In addition, we collected data from previous studies to compare and situate our work with existing knowledge.ResultsIn three of four families, novel deleterious variants have been identified in three different genes, including ZDHHC9 (p. Leu189Pro), ATP2B3 (p. Asp847Glu), and GLRA2 (p. Arg350Cys) and also with new clinical features and in another one family, a reported pathogenic variant in the L1CAM (p. Glu309Lys) gene has been identified related to new clinical findings.ConclusionThe current study's findings expand the existing knowledge of variants of the genes implicated in XLID and broaden the spectrum of phenotypes associated with the related conditions. The data have implications for genetic diagnosis and counseling.

FRI256 The Clinical Impacts Of Bi-allelic Germline Pathogenic Variant In TP53 In Two Patients With Li-Fraumeni Syndrome

Abstract Disclosure: V. Petry: None. D. Cohn: None. R.R. Oppenheimer: None. M.D. Estevez-Diz: None. A. Latronico: None. B.B. Mendonca: None. M.Q. Almeida: None. M.C. Fragoso: None. Background: Li-Fraumeni syndrome is an autosomal dominant cancer predisposition due to a heterozygous germline TP53 mutation. This mutation is related to different types of cancer; mainly adrenocortical carcinomas (ACC), soft tissues and bone sarcomas, breast cancer, choroid plexus carcinoma and leukemias at early ages. Although little is known about the impact of this TP53 variant in the homozygous form. Methods: We described the clinical presentation and the follow-up of 2 patients with a TP53 (p.R337H) homozygous pathogenic variant inherited from their parents. Case 1: A two year old patient presented with a headache, vomiting and nuchal stiffness, and was taken to the ER where she had a CNS CT scan. The CT scan revealed a mass located at left intraventricular region She then had surgery to remove the tumor and the histological finding confirmed the diagnosis of choroid plexus carcinoma. She underwent adjuvant systemic chemotherapy Headstart III protocol. This was the first case of cancer within this family. The child was seen by a medical geneticist and a genetic test revealed a homozygous pathogenic variant (p.R337H) in TP53. Afterwards her parents were tested and both were heterozygous for the p.R337H mutation. The patient is now 4 years old and free of oncologic disease. Case 2: A 9 months old female patient presented with Cushing´s syndrome and heterosexual precocious puberty. The MRI revealed a right adrenal tumor and she underwent laparoscopic adrenalectomy. Oral hydrocortisone was initiated postoperatively as glucocorticoid replacement therapy and was gradually tapered off over 6 months. Both parents of the patient were heterozygous for the p.R337H mutation in TP53 and they reported several cases of cancer within the family. The patient inherited both mutated alleles TP53 p.R337H. She had normal puberty development and she reached the target height. The patient did not develop further neoplasms during long-term follow-up (23 years). Conclusions: We described 2 cases with a biallelic pathogenic variant in TP53 (p.R337H) who were diagnosed with cancer at early ages and who did not develop further neoplasms during the follow-up period. There is a previous case description in the literature of a patient with a homozygous p.R337H mutation in TP53 who developed ACC at an early age and he did not develop other neoplasms during 8 years of follow-up. These two cases draw your attention to the early age for the development of choroid plexus carcinoma and adrenocortical tumors as well as the published case by Giacomazzi et al. Whether the bi-allelic pattern of the TP53 variant influences the tumor’s behavior remains unclear, there are potentially broad implications for clinical surveillance and genetic counseling for patients and their families. Presentation: Friday, June 16, 2023

Major Cardiac Events in Patients and Relatives With Hereditary Hypertrophic Cardiomyopathy

BackgroundLittle evidence is available on the disease expression in relatives of index patients with hypertrophic cardiomyopathy (HCM). This information has important implications for family screening programs, genetic counseling, and management of affected families. ObjectivesThe purpose of this study was to investigate the disease expression and penetrance in relatives of index patients carrying pathogenic/likely pathogenic (P/LP) variants in recognized HCM genes. MethodsA total of 453 consecutive and unrelated HCM index patients underwent clinical and genetic investigations. A total of 903 relatives of genotype-positive index patients were invited for clinical investigations and genetic testing. Penetrance, disease expression, and incidence rates of major adverse cardiac events (MACEs) were investigated in individuals carrying P/LP variants. ResultsForty percent (183/453) of index patients carried a P/LP variant. Eighty-four percent (757/903) of all relatives of index patients with P/LP variants were available for the investigation, of whom 54% (407/757) carried a P/LP variant. The penetrance of HCM among relatives was 39% (160/407). Relatives with HCM and index patients were diagnosed at a similar age (43 ± 18 years vs 46 ± 15 years; P = 0.11). There were no differences in clinical characteristics or incidence rates of MACE during 8 years of follow-up. ConclusionsThe disease expression of HCM among index patients and affected relatives carrying P/LP variants in recognized disease genes was similar, with an equal risk of experiencing MACE. These findings provide evidence to support family screening and follow-up of genotype-positive HCM families to improve management and diminish the number of adverse disease complications among relatives.

Advancing precision oncology through systematic germline and tumor genetic analysis: The oncogenetic point of view on findings from a prospective multicenter clinical trial of 666 patients.

With the emergence of targeted therapies, there is a need to accurately identify more tumor biomarkers. The EXOMA trial was designed to offer tumor and germline exome sequencing (ES) to patients with solid malignant tumors and facing therapeutic failure. As hereditary cancer predispositions could be identified, with genetic counseling and health management implications, a genetic consultation was systematically established. This design needs to be discussed as genetic human resources are limited and indication of theranostic tests will increase. Genetic counseling was conducted within 15 days following inclusion in the study for patients recruited between December 2015 and July 2019. In silico analyses from theranostic ES were limited to 317 genes involved in oncogenesis, from both tumor and blood DNA. Six hundred and sixty six patients had a genetic consultation before ES. In 65/666 patients, 66 germline pathogenic or likely pathogenic (P/LP) variants were identified in 16 actionable genes and seven non-actionable genes according to French guidelines. 24/65 patients had previously received genetic analysis for diagnostic purposes, and for 17 of them, a P/LP variant had already been identified. Among the 48/65 remaining cases for which the EXOMA protocol revealed a previously unknown P/LP variant, only 19 met the criteria for genetic testing for inherited cancer risk after familial survey. These criteria had not been identified by the oncologist in 10 cases. In 21/65 cases, the variant was considered incidental. In 7.4% of patients, an undiagnosed hereditary genetic predisposition was identified, whether or not related to the clinical presentation, and germline analysis impacted oncological management for only 6.3% of the cohort. This low percentage should be weighed against the burden of systematic genetic consultation and urgent circuits. Information or training tools to form oncologists to the prescription of germline genetic analyses should be explored, as well as information supports and patient preferences.

A novel smoothed (SMO) point mutation in congenital tibial hemimelia: a case report

BackgroundCongenital tibial hemimelia (CTH [MIM: 275220]) is a rare congenital limb deficiency that manifests as a shortened, curved, dysplastic or absent tibia with polydactyly. In previous studies, mutations of a distant sonic hedgehog (SHH) cis-regulator (ZRS) and a Shh repressor (GLI3) were identified.Case presentationHere, we admitted a 20-month-old boy who manifested with right tibial deformity, varus foot, ankle dislocation, and ipsilateral preaxial polydactyly. After genetic sequencing and data analysis, the results revealed a 443 A > G mutation in the father and a 536 C > T mutation in the mother in exon 2 of the Smoothed (SMO) gene at 7q32.1, with the coexistence of both mutant alleles in the proband/patient.ConclusionsOur report suggests that even though not previously reported, SMO mutations may be associated with limb anomalies such as tibial hemimelia via Hh signaling in humans and has implications for genetic counseling.

Extended genetic analysis and tumor characteristics in over 4600 women with suspected hereditary breast and ovarian cancer

BackgroundGenetic screening for pathogenic variants (PVs) in cancer predisposition genes can affect treatment strategies, risk prediction and preventive measures for patients and families. For decades, hereditary breast and ovarian cancer (HBOC) has been attributed to PVs in the genes BRCA1 and BRCA2, and more recently other rare alleles have been firmly established as associated with a high or moderate increased risk of developing breast and/or ovarian cancer. Here, we assess the genetic variation and tumor characteristics in a large cohort of women with suspected HBOC in a clinical oncogenetic setting.MethodsWomen with suspected HBOC referred from all oncogenetic clinics in Sweden over a six-year inclusion period were screened for PVs in 13 clinically relevant genes. The genetic outcome was compared with tumor characteristics and other clinical data collected from national cancer registries and hospital records.ResultsIn 4622 women with breast and/or ovarian cancer the overall diagnostic yield (the proportion of women carrying at least one PV) was 16.6%. BRCA1/2 PVs were found in 8.9% of women (BRCA1 5.95% and BRCA2 2.94%) and PVs in the other breast and ovarian cancer predisposition genes in 8.2%: ATM (1.58%), BARD1 (0.45%), BRIP1 (0.43%), CDH1 (0.11%), CHEK2 (3.46%), PALB2 (0.84%), PTEN (0.02%), RAD51C (0.54%), RAD51D (0.15%), STK11 (0) and TP53 (0.56%). Thus, inclusion of the 11 genes in addition to BRCA1/2 increased diagnostic yield by 7.7%. The yield was, as expected, significantly higher in certain subgroups such as younger patients, medullary breast cancer, higher Nottingham Histologic Grade, ER-negative breast cancer, triple-negative breast cancer and high grade serous ovarian cancer. Age and tumor subtype distributions differed substantially depending on genetic finding.ConclusionsThis study contributes to understanding the clinical and genetic landscape of breast and ovarian cancer susceptibility. Extending clinical genetic screening from BRCA1 and BRCA2 to 13 established cancer predisposition genes almost doubles the diagnostic yield, which has implications for genetic counseling and clinical guidelines. The very low yield in the syndrome genes CDH1, PTEN and STK11 questions the usefulness of including these genes on routine gene panels.

MYT1L variant inherited by a mosaic father in a case of severe developmental and epileptic encephalopathy.

The MYT1L gene plays a critical role in brain development, promoting the differentiation and proliferation of cells, important for the formation of brain connections. MYT1L is also involved in regulating the development of the hypothalamus, which is a crucial actor in weight regulation. Genetic variants in the MYT1L are associated with a range of developmental disorders, including intellectual disability, autism spectrum disorder, facial dysmorphisms, and epilepsy. The specific role of MYT1L in epilepsy remains elusive and no patients with developmental and epileptic encephalopathy (DEE) have been described so far. In this study, we report a patient with DEE presenting with severe refractory epilepsy, obesity and behavioral abnormalities. Exome sequencing led to the identification of the heterozygous variant NM_001303052.2: c.1717G>A, p.(Gly573Arg) (chr2-1910340-C-T; GRCh38.p14) in the MYT1L gene. This variant was found to be inherited by the father, who was a mosaic and did not suffer from any neuropsychiatric disorders. Our observations expand the molecular and phenotype spectrum of MYT1L related disorders, suggesting that affected individuals may present with severe epileptic phenotype leading to neurocognitive deterioration. Furthermore, we show that mosaic parents may not display the disease phenotype, with relevant implications for genetic counseling.

Genetic counseling in diabetes mellitus: A practice resource of the National Society of Genetic Counselors.

Diabetes mellitus is a group of diseases characterized by hyperglycemia and its consequences, affecting over 34 million individuals in the United States and 422 million worldwide. While most diabetes is polygenic and is classified as type 1 (T1D), type 2 (T2D), or gestational diabetes (GDM), at least 0.4% of all diabetes is monogenic in nature. Correct diagnosis of monogenic diabetes has important implications for glycemic management and genetic counseling. We provide this Practice Resource to familiarize the genetic counseling community with (1) the existence of monogenic diabetes, (2) how it differs from more common polygenic/complex diabetes types, (3) the advantage of a correct diagnosis, and (4) guidance for identifying, counseling, and testing patients and families with suspected monogenic diabetes. This document is intended for genetic counselors and other healthcare professionals providing clinical services in any setting, with the goal of maximizing the likelihood of a correct diagnosis of monogenic diabetes and access to related care.

PUF60-related developmental disorder: A case series and phenotypic analysis of 10 additional patients with monoallelic PUF60 variants.

PUF60-related developmental disorder (also referred to as Verheij syndrome), resulting from haploinsufficiency of PUF60, is associated with multiple congenital anomalies affecting a wide range of body systems. These anomalies include ophthalmic coloboma, and congenital anomalies of the heart, kidney, and musculoskeletal system. Behavioral and intellectual difficulties are also observed. While less common than other features associated with PUF60-related developmental disorder, for instance hearing impairment and short stature, identification of specific anomalies such as ophthalmic coloboma can aid with diagnostic identification given the limited spectrum of genes linked with this feature. We describe 10 patients with PUF60 gene variants, bringing the total number reported in the literature, to varying levels of details, to 56 patients. Patients were recruited both via locally based exome sequencing from international sites and from the DDD study in the United Kingdom. Eight of the variants reported were novel PUF60 variants. The addition of a further patient with a reported c449-457del variant to the existing literature highlights this as a recurrent variant. One variant was inherited from an affected parent. This is the first example in the literature of an inherited variant resulting in PUF60-related developmental disorder. Two patients (20%) were reported to have a renal anomaly consistent with 22% of cases in previously reported literature. Two patients received specialist endocrine treatment. More commonly observed were clinical features such as: cardiac anomalies (40%), ocular abnormalities (70%), intellectual disability (60%), and skeletal abnormalities (80%). Facial features did not demonstrate a recognizable gestalt. Of note, but remaining of unclear causality, we describe a single pediatric patient with pineoblastoma. We recommend that stature and pubertal progress should be monitored in PUF60-related developmental disorder with a low threshold for endocrine investigations as hormone therapy may be indicated. Our study reports an inherited case with PUF60-related developmental disorder which has important genetic counseling implications for families.

Maternal mosaicism in SSBP1 causing optic atrophy with retinal degeneration: implications for genetic counseling

BackgroundOptic atrophy-13 with retinal and foveal abnormalities (OPA13) (MIM #165510) is a mitochondrial disease in which apparent bilateral optic atrophy is present and sometimes followed by retinal pigmentary changes or photoreceptors degeneration. OPA13 is caused by heterozygous mutation in the SSBP1 gene, associated with variable mitochondrial dysfunctions.ResultsWe have previously reported a 16-year-old Taiwanese male diagnosed with OPA13 and SSBP1 variant c.320G>A (p.Arg107Gln) was identified by whole exon sequence (WES). This variant was assumed to be de novo since his parents were clinically unaffected. However, WES and Sanger sequencing further revealed the proband’s unaffected mother carrying the same SSBP1 variant with a 13% variant allele frequency (VAF) in her peripheral blood. That finding strongly indicates the maternal gonosomal mosaicism contributing to OPA13, which has not been reported before.ConclusionsIn summary, we described the first case of OPA13 caused by maternal gonosomal mosaicism in SSBP1. Parental mosaicism could be a serious issue in OPA13 diagnosis, and appropriate genetic counseling should be considered.

Advantages of routine next-generation sequencing over standard genetic testing in the amyotrophic lateral sclerosis clinic.

Next-generation sequencing has enhanced our understanding of amyotrophic lateral sclerosis (ALS) and its genetic epidemiology. Outside the research setting, testing is often restricted to those who report a family history. The aim of this study was to explore the added benefit of offering routine genetic testing to all patients in a regional ALS centre. C9ORF72 expansion testing and exome sequencing was offered to consecutive patients (150 with ALS and 12 with primary lateral sclerosis [PLS]) attending the Oxford Motor Neuron Disease Clinic within a defined time period. A total of 17 (11.3%) highly penetrant pathogenic variants in C9ORF72, SOD1, TARDBP, FUS and TBK1 were detected, of which 10 were also found through standard clinical genetic testing pathways. The systematic approach resulted in five additional diagnoses of a C9ORF72 expansion (number needed to test [NNT] = 28), and two further missense variants in TARDBP and SOD1 (NNT = 69). Additionally, 3 patients were found to carry pathogenic risk variants in NEK1, and 13 patients harboured common missense variants in CFAP410 and KIF5A, also associated with an increased risk of ALS. We report two novel non-coding loss-of-function splice variants in TBK1 and OPTN. No relevant variants were found in the PLS patients. Patients were offered double-blinded participation, but >80% requested disclosure of the results. This study provides evidence that expanding genetic testing to all patients with a clinical diagnosis of ALS enhances the potential for recruitment to clinical trials, but will have direct resource implications for genetic counselling.

De novo variants implicate chromatin modification, transcriptional regulation, and retinoic acid signaling in syndromic craniosynostosis

Craniosynostosis (CS) is the most common congenital cranial anomaly. Several Mendelian forms of syndromic CS are well described, but a genetic etiology remains elusive in a substantial fraction of probands. Analysis of exome sequence data from 526 proband-parent trios with syndromic CS identified a marked excess (observed 98, expected 33, p= 4.83×10-20) of damaging de novo variants (DNVs) in genes highly intolerant to loss-of-function variation (probability of LoF intolerance>0.9). 30 probands harbored damaging DNVs in 21 genes that were not previously implicated in CS but are involved in chromatin modification and remodeling (4.7-fold enrichment, p= 1.1×10-11). 17 genes had multiple damaging DNVs, and 13 genes (CDK13, NFIX, ADNP, KMT5B, SON, ARID1B, CASK, CHD7, MED13L, PSMD12, POLR2A, CHD3, and SETBP1) surpassed thresholds for genome-wide significance. A recurrent gain-of-function DNV in the retinoic acid receptor alpha (RARA; c.865G>A [p.Gly289Arg]) was identified in two probands with similar CS phenotypes. CS risk genes overlap with those identified for autism and other neurodevelopmental disorders, are highly expressed in cranial neural crest cells, and converge in networks that regulate chromatin modification, gene transcription, and osteoblast differentiation. Our results identify several CS loci and have major implications for genetic testing and counseling.

Digital droplet PCR (ddPCR) to investigate parental mosaicism in New Zealand families with apparently de novo syndromic disorders

A recurrence risk of under 1% is usually quoted for parents of children who have apparently de novo genetic conditions. Since 2018, our service has offered digital droplet PCR (ddPCR) testing to determine parental mosaicism rates for apparently de novo variants identified in children with syndromic disorders Aim: To determine the rate of parental mosaicism in a cohort of New Zealand families with apparently de novo pathogenic variants. Method: Specific assays were designed for each pathogenic variant. DNA derived from varying combinations of leukocytes, urothelial buccal and semen was tested by ddPCR for the pathogenic variants identified in the affected children. Results: 102 trio cases have been analysed. Seven parents were identified as being mosaic (6.8%). There is a preponderance of paternal mosaicism (6 of 7 being paternally derived) and two couples had a recurrence of the condition in a second child. Conclusion: This small cohort demonstrates a higher rate of parental mosaicism compared to the typically quoted recurrence risk of <1% and has implications for genetic counselling and genetic testing provision.

Distrofias Hereditarias de Retina en España: tres décadas de estudio epidemiológico, clínico y genético

Inherited Retinal Dystrophies (IRDs) are a group of rare diseases with a prevalence of 1:3000-4000 people. They are genetic, primarily affecting retinal photoreceptors and epithelial pigmentary cells, and lead to neurodegeneration and finally apoptosis. In 2021, we published our global results obtained in our registry at the Fundación Jiménez Díaz University Hospital (Madrid, Spain) from 1991 to August 2019. Now, we aimed to update these results until August 2022. Thus, we conducted a retrospective hospital-based cross-sectional study on 4.794 IRD-affected unrelated families from all the Spanish autonomous communities. Families were classified into three phenotypic categories: a) “NON-RP” for cone-dominated phenotypes, b) “RP” (retinitis pigmentosa) for primary rod involvement, and c) “syndromic IRD” when visual plus extra-ocular symptoms are present. Molecular studies included: single-gene studies, clinical exome, whole exome or whole genome sequencing. Overall, 62% (2962/4794) of the families were genetically characterized, in which 1.997 different likely causative variants (5.064 different alleles) were identified in 188 genes. The most common phenotype encountered was RP (59% of families, 2465/4794). Regarding the types of causative alleles, missenses were the most frequent (51%), followed by truncating (nonsense, frameshift, indels and splicing; 44%), while copy number variations were only 2%. The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP families, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and MYO7A, USH2A and BBS1 in syndromic IRD. Pathogenic variants ABCA4:p.Arg1129Leu and USH2A:p.Cys759Phe were the most frequent. Our study provides the overall genetic landscape for IRD in Spain, reporting the largest cohort ever presented and a high number of causal genes involved in these diseases. Furthermore, our findings have important implications for genetic diagnosis and counseling, but also for possible therapeutic management

Feedback of individual genetic and genomics research results: A qualitative study involving grassroots communities in Uganda.

Genetics and genomics research (GGR) is associated with several challenges including, but not limited to, methods and implications of sharing research findings with participants and their family members, issues of confidentiality, and ownership of data obtained from samples. Additionally, GGR holds significant potential risk for social and psychological harms. Considerable research has been conducted globally, and has advanced the debate on return of genetic and genomics testing results. However, such investigations are limited in the African setting, including Uganda where research ethics guidance on return of results is deficient or suboptimal at best. The objective of this study was to assess perceptions of grassroots communities on if and how feedback of individual genetics and genomics testing results should occur in Uganda with a view to improving ethics guidance. This was a cross-sectional study that employed a qualitative exploratory approach. Five deliberative focus group discussions (FGDs) were conducted with 42 participants from grassroots communities representing three major ethnic groupings. These were rural settings and the majority of participants were subsistence farmers with limited or no exposure to GGR. Data were analysed through thematic analysis, with both deductive and inductive approaches applied to interrogate predetermined themes and to identify any emerging themes. NVivo software (QSR international 2020) was used to support data analysis and illustrative quotes were extracted. All the respondents were willing to participate in GGR and receive feedback of results conditional upon a health benefit. The main motivation was diagnostic and therapeutic benefits as well as facilitating future health planning. Thematic analysis identified four themes and several sub-themes including 1) the need-to-know health status 2) paternity information as a benefit and risk; 3) ethical considerations for feedback of findings and 4) extending feedback of genetics findings to family and community. Participation in hypothetical GGR as well as feedback of results is acceptable to individuals in grassroots communities. However, the strong therapeutic and/or diagnostic misconception linked to GGR is concerning given that hopes for therapeutic and/or diagnostic benefit are unfounded. Viewing GGR as an opportunity to confirm or dispute paternity was another interesting perception. These findings carry profound implications for consent processes, genetic counselling and research ethics guidance. Privacy and confidentiality, benefits, risks as well as implications for sharing need to be considered for such feedback of results to be conducted appropriately.

Redefining a Rare CNS Tumour Through Targeted Genetic Sequencing

Abstract AIMS Isolated cerebellar vermis lesions in adults is a rare location and entity with few literature case reports detailing gangliogliomas and gangliocytomas. Using targeted genetic sequencing, traditional histological diagnosis can be refined further, with a clear impact on prognosis as well as possible genetic counselling implications. METHOD A single case of cerebellar vermis lesion, identified incidentally through imaging of a neck nodule, with subtle features of ataxia and mild impairment of initiation of speech. Sub-total resection of lesion underwent standard histopathological work-up, followed by targeted genetic sequencing to obtain an integrated diagnosis. RESULTS Histological assessment identified atypical ganglion cells labelled with Synaptophysin on immunohistochemistry. Features closely resembled dysplastic cerebellar gangliocytoma (Lhermitte-Duclos Disease). Further targeted sequencing showed no evidence of IDH1, IDH2, TERT promoter, or histone mutation, however, BRAF mutation was present, supporting an alternate diagnosis of ganglioglioma. CONCLUSION Precision medicine is facilitated with advanced diagnostic techniques. This redefines categorisation of some CNS tumours, particularly rare entities. Techniques are especially valuable to individual patient management as they can have a direct impact on aspects of clinical work-up, prognosis, follow-up, and in some cases, genetic counselling.