Value Of Whole Exome Sequencing Research Articles

Application of whole exome sequencing for the inferential analysis of recessive genetic disease carrier status for couples with a child died of Primary immunodeficiency

To explore the value of whole exome sequencing for the inferential analysis of recessive genetic disease carrier status for couples with a child died of Primary immunodeficiency (PID). Clinical data was collected from four couples with a childbearing history of PID who had sought genetic counseling and undergone genetic testing at Henan Provincial People's Hospital from February 2017 to December 2021. Whole exome sequencing (WES) was performed on both partners of each couple, and candidate variants were validated by Sanger sequencing and fluorescent quantitative PCR. Prenatal diagnosis was conducted on fetuses of these couples after confirming the variants. A total of six variants were detected in four genes including IL2RG, BTK, CYBB, and DUOX2. Among these, the c.1265G>A and c.3329G>A variants of the DUOX2 gene and the c.676C>T variant of the IL2RG gene were previously known as pathogenic variants. On the other hand, the Exon5_8del variant of the IL2RG gene, the c.184_185delAC variant of the BTK gene, and the c.472A>T variant of the CYBB gene were unreported previously. Based on the guidelines from the American College of Medical Genetics and Genomics, the IL2RG: Exon5_8del, BTK: c.184_185delAC and CYBB: c.472A>T variants were classified as likely pathogenic (PVS1+PM2_Supporting+PP4).Prenatal diagnosis was conducted for three couples during their subsequent pregnancies, and the results revealed that the fetuses had the wild-type genotypes at the c.184_185 position of the BTK gene, the c.472 position of the CYBB gene, and the c.676 position of the IL2RG gene. Follow-up examinations one year after birth has found no abnormality in the infants. WES is an important tool to infer and analyze the carrier status for couples who had given births to children died of PID and improve the positive detection rate.

Diagnosis of Primary Ciliary Dyskinesia via Whole Exome Sequencing and Histologic Findings.

To assess the diagnostic potential of whole-exome sequencing (WES) and elucidate the clinical and genetic characteristics of primary ciliary dyskinesia (PCD) in the Korean population. Forty-seven patients clinically suspected of having PCD were enrolled at a tertiary medical center. WES was performed in all patients, and seven patients received biopsy of cilia and transmission electron microscopy (TEM). Overall, PCD was diagnosed in 10 (21.3%) patients: eight by WES (8/47, 17%), four by TEM. Among patients diagnosed as PCD based on TEM results, two patients showed consistent results with WES and TEM of PCD (2/4, 50%). In addition, five patients, who were not included in the final PCD diagnosis group, had variants of unknown significance in PCD-related genes (5/47, 10.6%). The most frequent pathogenic (P)/likely pathogenic (LP) variants were detected in DNAH11 (n=4, 21.1%), DRC1 (n=4, 21.1%), and DNAH5 (n=4, 21.1%). Among the detected 17 P/LP variants in PCD-related genes in this study, 8 (47.1%) were identified as novel variants. Regarding the genotype-phenotype correlation in this study, the authors experienced severe PCD cases caused by the LP/P variants in MCIDAS, DRC1, and CCDC39. Through this study, we were able to confirm the value of WES as one of the diagnostic tools for PCD, which increases with TEM, rather than single gene tests. These results will prove useful to hospitals with limited access to PCD diagnostic testing but with relatively efficient in-house or outsourced access to genetic testing at a pre-symptomatic or early disease stage.

Whole exome sequencing identifies novel pathogenic variants in TGM1 and ALOX12B in patients with hereditary ichthyosis.

Hereditary ichthyosis is a clinically and genetically heterogeneous disorder associated with more than 50 genes with TGM1, ALOX12B, and ALOXE3 being the most prevalent. Establishing an accurate diagnosis is important for effective genetic counseling and optimal patient management. We studied the diagnostic value of whole exome sequencing (WES) in a small case series with hereditary ichthyosis. During a 1-year period, index cases of 5 unrelated families clinically diagnosed with hereditary ichthyosis went through WES, followed by extensive segregation analysis. Prenatal diagnosis (PND) was conducted where indicated. We identified 4 homozygous variants-2 in TGM1 (c.655A>G and c.797A>G) and 2 in ALOX12B (c.527+2T>G and c.1654G>T)-alongside a heterozygous variant in TGM1 (c.428G>A) in 5 families. The variants were all pathogenic/likely pathogenic according to the ACMG classification and segregation analysis, except for c.797A>G in TGM1 which remained a variant of unknown clinical significance. Four variants were novel. All families were referred either during pregnancy or before reproductive planning; 4 benefited from WES as it identified the mutation in the probands and enabled carrier detection in at-risk relatives; PND was conducted in 2 families. Our findings further support WES is a powerful tool for the comprehensive, accurate, and rapid molecular diagnosis of hereditary ichthyosis and can offer opportunities for reproductive planning, carrier screening and prenatal diagnosis to at-risk families.

SAT613 A Novel NF1 Mutation As The Underlying Cause Of Dysmorphic Features And Acromegaly In An Atypical Case Of Neurofibromatosis Type 1

Abstract Disclosure: O. Alsagheir: None. L.A. Alobaid: None. M. Alswailem: None. H. Al-Hindi: None. A.S. Alzahrani: None. Introduction: Neurofibromatosis type 1 is an autosomal dominant disease with an estimated incidence of about 1:2000 cases. It is caused by genetic alterations in the gene NF1 encoding the tumor suppressor gene, neurofibromin. Patients with neurofibromatosis 1 are at an increased risk of a number of benign and malignant tumors including optic nerve gliomas, CNS tumors, malignant peripheral nerve sheath tumors, pheochromocytomas and many others. However, pituitary adenomas have been rarely described in neurofibromatosis type 1 and NF1 mutations have been found rarely in patients without manifestations of neurofibromatosis. In this report, we describe a patient with acromegaly who had some dysmorphic features but no clear skin or other manifestations of neurofibromatosis. He was found to have a deletion mutation in NF1 suggesting that his dysmorphic features and acromegaly are atypical manifestations of a previously undiagnosed neurofibromatosis type 1. Case Description: A 26-year-old-man presented at 18 years of age for evaluation of possible ventricular septal defect, which was ruled out by echocardiography, but he was found to have a subaortic membrane with moderate aortic regurgitation. He was also noticed to have coarse facial and body features which raised the possibility of acromegaly. He didn’t notice any facial changes, change in the size of hands and feet, headache or visual disturbances. In the family history, he reported that a number of his siblings are tall with large body habitus; none of them was evaluated or known to have medical illness. Physical examination: height 184 cm, weight 87 Kg, BMI 25, and BP 117/77 mmHg. He has frontal bossing, large supraorbital ridges, macrognathia, and hoarse deep voice but no skin tags, café au let spots, skin fibromas or freckling. Eye examination was unremarkable. Investigations: IGF-1 415 ng/ml (188-400), random GH 1.09 ng.ml (0.1-1.2). An oral glucose tolerance test showed baseline GH 0.99 increased to 8.05 ng/ml. An MRI of the pituitary gland showed a lobulated sellar and suprasellar heterogeneously enhancing pituitary adenoma. A Gallium 68 PET-CT scan showed an intense focus of uptake at the same location. Whole exome sequencing revealed a heterozygous NF1 mutation (NM_001128147.3: c.1782_*2del). This variant is likely pathogenic according to ACMG criteria. Conclusion: This case illustrates the value of whole exome sequencing for genetic testing in diagnosing atypical dysmorphia and other conditions when the diagnosis is not clear on clinical evaluation or conventional investigations. It also describes a rare association of acromegaly with neurofibromatosis. Presentation: Saturday, June 17, 2023

Clinical and genetic screening in a large Iranian family with Marfan syndrome: A case study.

Marfan syndrome (MFS) is an autosomal dominant genetic disorder caused by pathogenic variants of the fibrillin-1-encoding FBN1 gene that commonly affects the cardiovascular, skeletal, and ocular systems. This study aimed to evaluate the clinical features and genetic causes of the MFS phenotype in a large Iranian family. Seventeen affected family members were examined clinically by cardiologists and ophthalmologists. The proband, a 48-year-old woman with obvious signs of MFS, her DNA sample subjected to whole-exome sequencing (WES). The candidate variant was validated by bidirectional sequencing of proband and other available family members. In silico analysis and molecular modeling were conducted to determine the pathogenic effects of the candidate variants. The most frequent cardiac complications are mitral valve prolapse and regurgitation. Ophthalmic examination revealed iridodonesis and ectopic lentis. A heterozygous missense variant (c.2179T>C/p.C727R) in exon 19 of FBN1 gene was identified and found to cosegregate with affected family members. Its pathogenicity has been predicted using several in silico predictive algorithms. Molecular docking analysis indicated that the variant might affect the binding affinity between FBN1 and LTBP1 proteins by impairing disulfide bond formation. Our report expands the spectrum of the Marfan phenotype by providing details of its clinical manifestations and disease-associated molecular changes. It also highlights the value of WES in genetic diagnosis and contributes to genetic counseling in families with MFS.

Whole-exome sequencing enables rapid and prenatal diagnosis of inherited skin disorders

BackgroundGenodermatoses are a broad group of disorders with specific or non-specific skin-based phenotypes, most of which are monogenic disorders. However, it’s a great challenge to make a precise molecular diagnosis because of the clinical heterogeneity. The genetic and clinical heterogeneity brings great challenges for diagnosis in dermatology. The whole exome sequencing (WES) not only expedites the discovery of the genetic variations, but also contributes to genetic counselling and prenatal diagnosis.Materials and methodsFollowed by the initial clinical and pathological diagnosis, genetic variations were identified by WES. The pathogenicity of the copy number variations (CNVs) and single-nucleotide variants (SNVs) were evaluated according to ACMG guidelines. Candidate pathogenic SNVs were confirmed by Sanger sequencing in the proband and the family members.ResultsTotally 25 cases were recruited. Nine novel variations, including c.5546G > C and c.1457delC in NF1, c.6110G > T in COL7A1, c.2127delG in TSC1, c.1445 C > A and c.1265G > A in TYR, Xp22.31 deletion in STS, c.908 C > T in ATP2A2, c.1371insC in IKBKG, and nine known ones were identified in 16 cases (64%). Prenatal diagnosis was applied in 6 pregnant women by amniocentesis, two of whom carried positive findings.ConclusionsOur findings highlighted the value of WES as a first-tier genetic test in determining the molecular diagnosis. We also discovered the distribution of genodermatoses in this district, which provided a novel clinical dataset for dermatologists.

Intronic position +9 and −9 are potentially splicing sites boundary from intronic variants analysis of whole exome sequencing data

Whole exome sequencing (WES) can also detect some intronic variants, which may affect splicing and gene expression, but how to use these intronic variants, and the characteristics about them has not been reported. This study aims to reveal the characteristics of intronic variant in WES data, to further improve the clinical diagnostic value of WES. A total of 269 WES data was analyzed, 688,778 raw variants were called, among these 367,469 intronic variants were in intronic regions flanking exons which was upstream/downstream region of the exon (default is 200 bps). Contrary to expectation, the number of intronic variants with quality control (QC) passed was the lowest at the +2 and −2 positions but not at the +1 and −1 positions. The plausible explanation was that the former had the worst effect on trans-splicing, whereas the latter did not completely abolish splicing. And surprisingly, the number of intronic variants that passed QC was the highest at the +9 and −9 positions, indicating a potential splicing site boundary. The proportion of variants which could not pass QC filtering (false variants) in the intronic regions flanking exons generally accord with “S”-shaped curve. At +5 and −5 positions, the number of variants predicted damaging by software was most. This was also the position at which many pathogenic variants had been reported in recent years. Our study revealed the characteristics of intronic variant in WES data for the first time, we found the +9 and −9 positions might be a potentially splicing sites boundary and +5 and −5 positions were potentially important sites affecting splicing or gene expression, the +2 and −2 positions seem more important splicing site than +1 and −1 positions, and we found variants in intronic regions flanking exons over ± 50 bps may be unreliable. This result can help researchers find more useful variants and demonstrate that WES data is valuable for intronic variants analysis.

Diagnostic value of whole exome sequencing for patients with intellectual disability or global developmental delay

To assess the diagnostic value of whole exome sequencing (WES) for patients with intellectual disability (ID) or global developmental delay (GDD). 134 individuals with ID or GDD who presented at Chenzhou First People's Hospital between May 2018 and December 2021 were selected as the study subjects. WES was carried out on peripheral blood samples of the patients and their parents, and candidate variants were verified by Sanger sequencing, copy number variation sequencing (CNV-seq) and co-segregation analysis. The pathogenicity of the variants was predicted based on the guidelines from the American College of Medical Genetics and Genomics (ACMG). A total of 46 pathogenic single nucleotide variants (SNVs) and small insertion/deletion (InDel) variants, 11 pathogenic genomic copy number variants (CNVs), and 1 uniparental diploidy (UPD) were detected, which yielded an overall detection rate of 43.28% (58/134). The 46 pathogenic SNV/InDel have involved 62 mutation sites in 40 genes, among which MECP2 was the most frequent (n = 4). The 11 pathogenic CNVs have included 10 deletions and 1 duplication, which have ranged from 0.76 to 15.02 Mb. A loss of heterozygosity (LOH) region of approximately 15.62 Mb was detected in 15q11.2q12 region in a patient, which was validated as paternal UPD based on the result of trio-WES. The patient was ultimately diagnosed as Angelman syndrome. WES can detect not only SNV/InDel, but also CNV and LOH. By integrating family data, WES can accurately determine the origin of the variants and provide a useful tool for uncovering the genetic etiology of patients with ID or GDD.

Whole exome sequencing analysis and prenatal diagnosis in children with neurodevelopmental disorders

To explore the application value of whole exome sequencing (WES) in the diagnosis of prenatal and postnatal neurodevelopmental disorders (NDDs). A total of 70 patients diagnosed with NDDs who underwent WES at the Medical Genetics Center of the Maternal and Child Health Hospital of Hubei Province between June 2020 and July 2021 were retrospectively analyzed. Genomic DNA was extracted from peripheral blood samples and amniotic fluid. WES-based copy number variant (CNV) analysis was integrated into the routine WES data analysis pipeline. The results showed that a molecular diagnosis rate could be made in 21/70 (30%) cases. Of 21 positive cases, 14 (23%) cases were detected by single-nucleotide variant/small insertion/deletion (SNV/Indel) analysis, of which 12 variants were novel, 6 (9.8%) cases were detected by WES-based CNV analysis, and 1 (1.6%) case was detected by a combination of both. The diagnostic yield of WES combined with CNV analysis was higher than that of SNV/Indel analysis alone (30%, 21/70 vs. 20%, 14/70). Of the 28 prenatally diagnosed cases, 6 cases were found to have inherited parental variation for NDDs, 10 cases were found not to have the same pathogenic variation as the proband, and the remaining 12 cases were found to have no pathogenic or likely pathogenic variation that could explain the NDDs phenotype. Clinical follow-up showed that 5 families opted for abortion and the remaining had no current abnormalities. In conclusion, WES may be an effective method to clarify the genetic etiology and prenatal diagnosis of NDDs, which is helpful in assessing the prognosis to aid clinical management and reproductive guidance.

Genetic variations in the DYNC2H1 gene causing SRTD3 (short-rib thoracic dysplasia 3 with or without polydactyly).

Background and aims: Short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3) represents a type of severe fetal skeletal dysplasia (SD) characterized by shortened limbs, narrow thorax with or without polydactyly, which is caused by the homozygous or compound heterozygous mutations in the DYNC2H1 gene. SRTD3 is a recessive disorder, identification of the responsible genetic variation would be beneficial to an accurate prenatal diagnosis and well-grounded counseling for the affected families. Material and methods: Two families having experienced recurrent fetal SDs were recruited and submitted to a multiplatform genetic investigation. Whole-exome sequencing (WES) was performed with samples collected from the probands. Sanger sequencing and fluorescent quantitative PCR (qPCR) were conducted as validation assays for suspected variations. Results: WES identified two compound heterozygous variations in the DYNC2H1(NM_001080463.2) gene, namely c.2386C>T (p.Arg796Trp) and c.7289T>C (p.Ile2430Thr) for one; and exon (64-83)del and c.8190G>T (p.Leu2730Phe) for the other, respectively. One variant in them, exon (64-83)del, was novelly identified. Conclusion: The study detected two compound heterozygous variation in DYNC2H1 including one novel deletion: exon (64-83) del. Our findings clarified the cause of fetal skeletal dysplasia in the subject families, provided guidance for their future pregnancies, and highlighted the value of WES in diagnosis of skeletal dysplasia with unclear prenatal indications.

Application value of whole exome sequencing in screening and identifying novel mutations of hypopharyngeal cancer

The research on targeted therapy of hypopharyngeal cancer is very scarce. The discovery of new targeted driver genes will promote the progress of hypopharyngeal cancer therapy to a great extent. In our research, whole-exome sequencing in 10 patients with hypopharyngeal cancer was performed to identify single nucleotide variations (SNVs) and insertions and deletions (INDELs). American College of Medical Genetics and Genomics (ACMG) guidelines were used to evaluate the pathogenicity of the selected variants. 8113 mutation sites in 5326 genes were identified after strict screening. We identified 72 pathogenic mutations in 53 genes according to the ACMG guidelines. Gene Ontology (GO) annotation and KEGG enrichment analysis show the effect of these genes on cancer. Protein–protein interaction (PPI) was analyzed by string online software. The validation results of the ualcan database showed that 22 of the 53 genes may be related to the poor prognosis of patients with hypopharyngeal cancer. RBM20 has the most significant correlation with hypopharyngeal cancer, and it is likely to be the driver gene of hypopharyngeal cancer. In conclusion, we found possible therapeutic targets for hypopharyngeal cancer, especially RBM20 and KMT2C. Our study provides a basis for the pathogenesis and targeted therapy of hypopharyngeal cancer.

Whole exome sequencing improves genetic diagnosis of fetal clubfoot.

This retrospective study aimed to investigate the value of whole exome sequencing (WES) for clubfoot (CF) fetuses with or without other structural abnormalities and to further explore the genetic causes of fetal CF. this study included 83 singleton pregnancies diagnosed with fetal CF referred to our center between January 2016 and March 2022; cases were divided into two groups: isolated CF and non-isolated CF. After excluding cases with positive karyotyping and chromosomal microarray analysis results, WES was performed for the eligible fetuses and parents. Monogenic variants detected by WES and perinatal outcomes were recorded and evaluated at postnatal follow-up. overall, clinically significant variations were identified in 12.0% (10/83) of fetuses, and the detection rate was significantly higher in the non-isolated than in the isolated CF group (8/36, 22.2% vs. 2/47, 4.3%, p = 0.031). We additionally detected eight (9.6%) fetuses harboring variants of unknown significance. We identified 11 clinically significant variations correlating with clinical phenotypes in nine genes from ten fetuses, with KLHL40 being the most frequent (n = 2). Furthermore, we observed a significant difference in termination and survival rates between isolated and non-isolated CF cases (27.6 vs. 77.8% and 59.6 vs. 19.4%, p < 0.001 for both). our data indicate that WES has a high additional diagnostic yield for the molecular diagnosis of fetal CF, markedly enhancing existing prenatal diagnostic capabilities and expanding our understanding of intrauterine genetic disorders, thus assisting us to better interpret fetal phenotype in the future.

P-560 Diagnostic value of whole exome sequencing (WES) in case of recurrent pregnancy losses

Abstract Study question Is it justified during genetic counseling to inform families with recurrent pregnancy losses about the possibility of testing abortion material using the WES method? Summary answer Informed families have the opportunity to find the monogenic cause of recurrent pregnancy losses with subsequent PGT-M analysis of embryos to prevent it. What is known already Despite WES is not recommended for recurrent pregnancy losses as a routine procedure, there are more and more data in favor of the practice. Study design, size, duration This is a retrospective study from 2019 to 2021 including 21 cases that were negative in case of routine karyotyping or aCGH. Three of them (14,3%) were found the cause of diseases by using WES. The study is ongoing. Participants/materials, setting, methods Whole exome sequencing of abortion material, chorionic villi specimens. Main results and the role of chance Family 1 has a history of euploid fetuses losses during the pregnancy. An autosomal recessive disease, Smith-Lemli-Opitz syndrome type II with early lethality (MIM 270400) was revealed by WES Trio at the 6th pregnancy loss case (mutations detected: c.964-1G&amp;gt;C and c.651C&amp;gt;A in DHCR7 gene in compound heterozygote state). The parents are Ashkenazi Jews and heterozygous carriers of a mutation in the same gene. The risk of pregnancy loss or stillbirth is 25%, and pregnancy planning by IVF with PGT-M is recommended. Family 2 has recurrent pregnancy losses, happening up to 11 weeks. A child was born with cardioencephalomyopathy, fatal infantile, due to cytochrome C oxidase deficiency 1 (MIM 604377). Mutation: c.418G&amp;gt;A in SCO2 gene in a homozygous state. The mutation was previously described as the cause of missed abortion. For family 3 was performed WES of abortus with congenital pathology. Mutation c.8263delC in Ciliary dyskinesia, primary, 40 (MIM 618300) gene DNAH9 in homo/heterozygous state. The mutation can result in malformations and stops in pregnancy development. The family is suggested to perform IVF with PGT-M. Limitations, reasons for caution The low detection frequency of monogenic causes of pregnancy losses and the high cost of the testing does not allow the use of WES of abortion material as a screening method. Wider implications of the findings Performing the WES helps to identify the high risks of monogenic pathology in the families. Changing reproductive tactics and pregnancy planning by IVF with PGT-M is recommended for early prevention of severe congenital pathology, stillbirth, malformations during pregnancy, recurrent pregnancy losses and reduction of the time to achieve healthy childbearing. Trial registration number not applicable

Identification of a Rare Variant of c.1777G>A (p.G593S) in the COL1A1 Gene as the Etiology of Recurrent Osteogenesis Imperfecta by Whole-Exome Sequencing.

BackgroundOsteogenesis imperfecta (OI) is a rare heterogeneous disorder typically featured by fragile bones and susceptibility to fracture. The aim of the present study was to explore the genetic etiology of familial recurrent OI and the genotype–phenotype correlation.MethodsKaryotyping, chromosomal microarray analysis, and whole-exome sequencing (WES) were performed to determine the genetic etiology of OI in the enrolled family. Western blotting analysis was carried out using the fetal skin tissue for type I collagen production analysis.ResultsAt the first pregnancy, a c.1777G>A mutation in the COL1A1 gene was detected in the fetus who exhibited skeletal dysplasia. In this second pregnancy, severe fetal skeletal dysplasia was also presented without significant chromosomal abnormality detected by karyotype and chromosomal microarray analysis in the fetus. Further WES results demonstrated a de novo missense mutation of c.1777G>A (p.G593S) in the fetus, which was classified as a pathogenic variant according to the ACMG guidelines. The recurrent mutation in the two fetuses hinted at the possible existence of gonadal mosaicism in the parents, while no mutation in the COL1A1 gene was identified in the DNA from the father's sperm. In addition, Western blot results demonstrated no reduced type I procollagen production in the affected fetus compared with the age-matched controls.ConclusionsTo the best of our knowledge, this is the first study that identified a rare variant of c.1777G>A in the COL1A1 gene that led to recurrent OI in the Chinese population. Additionally, we believe that this rare variant of c.1777G>A in the COL1A1 gene will lead to OI type II. The results of the present study further verify the application value of WES in identifying fetuses with ultrasound anomalies.

Exome-based mutation screening in South African children with primary congenital glaucoma.

To identify pathogenic variants in a cohort of 23 black South African children with sporadic primary congenital glaucoma (PCG) using an exome-based approach. Children with PCG were recruited from two Paediatric Ophthalmology Clinics in Johannesburg, South Africa. Whole exome sequencing was performed on genomic DNA. Of the 23 children, 19 were male and 19 had bilateral PCG. A variant prioritization strategy was employed whereby variants in known PCG genes (CYP1B1, LTBP2 and TEK) were evaluated first, followed by the identification of putative disease-causing variants in other genes related to eye diseases and phenotypes. Validated pathogenic variants in the CYP1B1 gene (c.1169 G>A; p.Arg390His) and TEK gene (c.922 G>A; p.Gly308Arg) were identified in one child each. No LTBP2 mutations were identified in this cohort. In silico predictions identified potentially damaging rare variants in genes previously associated with eye development phenotypes or glaucoma in a further 12 children. This study demonstrates the value of whole exome sequencing in identifying disease-causing variants in African children with PCG. It is the first report of a TEK disease-causing variant in an African PCG patient. Potential causative variants detected in PCG candidate genes warrant further investigation.

Predicting pathogenicity for novel hearing loss mutations based on genetic and protein structure approaches

Hearing loss is a heterogeneous disorder. Identification of causative mutations is demanding due to genetic heterogeneity. In this study, we investigated the genetic cause of sensorineural hearing loss in patients with severe/profound deafness. After the exclusion of GJB2-GJB6 mutations, we performed whole exome sequencing in 32 unrelated Argentinean families. Mutations were detected in 16 known deafness genes in 20 patients: ACTG1, ADGRV1 (GPR98), CDH23, COL4A3, COL4A5, DFNA5 (GSDDE), EYA4, LARS2, LOXHD1, MITF, MYO6, MYO7A, TECTA, TMPRSS3, USH2A and WSF1. Notably, 11 variants affecting 9 different non-GJB2 genes resulted novel: c.12829C > T, p.(Arg4277*) in ADGRV1; c.337del, p.(Asp109*) and c.3352del, p.(Gly1118Alafs*7) in CDH23; c.3500G > A, p.(Gly1167Glu) in COL4A3; c.1183C > T, p.(Pro395Ser) and c.1759C > T, p.(Pro587Ser) in COL4A5; c.580 + 2 T > C in EYA4; c.1481dup, p.(Leu495Profs*31) in LARS2; c.1939 T > C, p.(Phe647Leu), in MYO6; c.733C > T, p.(Gln245*) in MYO7A and c.242C > G, p.(Ser81*) in TMPRSS3 genes. To predict the effect of these variants, novel protein modeling and protein stability analysis were employed. These results highlight the value of whole exome sequencing to identify candidate variants, as well as bioinformatic strategies to infer their pathogenicity.

Analysis of families with fetal congenital abnormalities but negative prenatal diagnosis by whole exome sequencing

Objective: To evaluate the value of whole exome sequencing (WES) in prenatal clinical application. Methods: A total of 1 152 cases of congenital abnormal [including structural malformation, nuchal translucency (NT) thickening and intrauterine growth restriction] with traditional prenatal diagnosis [including G-band karyotype analysis and chromosome microarray analysis (CMA)] negative were analyzed. The congenital abnormal fetuses were divided into retrospective group and prospective group according to the time of WES detection, that is whether the pregnancy termination or not. According to the specific location of fetal malformation and their family history, the cohort was divided into subgroups. The clinical prognosis of all fetuses were followed up, and the effect of WES test results on pregnancy decision-making and clinical intervention were analyzed. According to the follow-up results, the data of fetuses with new phenotypes in the third trimester or after birth were re-analyzed. Results: Among 1 152 families who received WES, 5 families were excluded because of nonbiological parents. Among the remaining 1 147 families, 152 fetuses obtained positive diagnosis (13.3%,152/1 147), including 74 fetuses in the retrospective group (16.1%,74/460) and 78 fetuses in the prospective group (11.4%,78/687). In fetuses with negative CMA and G-band karyotype analysis results but new phenotypes in the third trimester or after birth, the positive rate by WES data re-analysis was 4.9% (8/163). A total of 34 (21.3%, 34/160) fetuses were directly affected by the corresponding positive molecular diagnosis. Among 68 cases of live births with diagnostic variation grade 4, 29 cases (42.7%, 29/68) received appropriate medical intervention through rapid review of WES results. Conclusions: WES could increase the detection rate of abnormal fetuses with negative G-banding karyotype analysis and CMA by 13.3%. Prenatal WES could guide pregnancy decision-making and early clinical intervention. It might be an effective strategy to pay attention to the special follow-up of the third trimester and postnatal fetus and to re-analyze the WES data.

Whole-exome sequencing increases the diagnostic rate for prenatal fetal structural anomalies

BackgroundPrenatal whole-exome sequencing (WES) is becoming increasingly used when karyotype and microarray tests are not diagnostic of fetal malformations. Although the value of WES clearly emerges in terms of higher diagnostic rates, the limitations of prenatal phenotyping together with the counseling challenges for variants of uncertain significance and incidental results suggest that the routine application of prenatal WES is not yet easy. MethodsStructurally abnormal fetuses with a mean gestational age of 24 weeks (range 13–38 weeks) were recruited from the Chong Qing Health Center for Women and Children. We performed a retrospective WES investigation in 85 fetuses, using DNA from amniotic fluid (66 samples, 77.6%), umbilical cord blood (10 samples, 11.8%), and fetal tissues (9 samples, 10.6%). Parental DNA was extracted from peripheral blood. ResultsMolecular diagnosis was obtained in 16 of the 85 fetuses (18.8%). According to the variant segregation mode and family history, 7 fetuses (43.75%) were affected by an autosomal dominant condition (6 variants were de novo and 1 variant was inherited from an unknowingly affected father), 7 fetuses (43.75%) had an autosomal recessive syndrome always associated with compound heterozygosity, and 2 fetuses (12.5%) had an X-linked condition (one mother was a carrier). In addition, the highest diagnostic rate was observed in fetuses with multisystem abnormalities (38.9%, 7/18). A variant of uncertain significance was detected in 16 samples (18.8%, 16/85). ConclusionOur study confirms that prenatal WES is an efficient tool for studying fetal abnormalities, although further improvements are needed to establish stronger fetal genotype-phenotype correlations.

Explore the value of whole exome sequencing in early diagnosis for children with language delay/disorder

Objective: To evaluate the utility of whole-exome sequencing (WES) in early diagnosis for children with language delay/disorder. Methods: Children with language delay/disorder who were admitted to the Department of Health Care, Children's Hospital Affiliated to the Capital Pediatric Institute from January 2019 to December 2020 were analyzed retrospectively. Based on informed consent, the peripheral blood of the children and their parents was collected for WES. Combining the clinical phenotypes of the children, the candidate variants, including single nucleotide variants (SNVs) and copy number variations (CNVs), were selected for validation and family segregation analysis using Sanger sequencing, real-time PCR or CNV-Seq. The pathogenicity of variants was evaluated based on ACMG guideline following with finial genetic diagnosis. Based on whether genetic diagnosis was achieved or not, 125 children with comprehensive examination of the Children Neuropsychological and Behavioral Scale(CNBS-R2016) were sub-grouped (positive/negative group), and the total scores and the detailed scores of five developmental sections (gross motor, fine motor, adaptive ability, language and social behavior ability) between two subgroups were compared. Results: A total of 165 children with language delay/disorder were recruited, including 109 males and 56 females. The ratio of boys to girls was 1.95∶1.The age of the children was (3.2±1.2) years old, the median age was 3.0 years. 45 children carry disease-related pathogenic/likely pathogenic variants, including 36 SNVs and 9 CNVs. The genetic diagnostic yield of this cohort was 27.3% (45/165). The inheritance analysis for core family members showed de novo variant accounted for 86% of genetic diagnosis (31/36). The positive diagnosis rate in girls was 45% (25/56), which was significantly higher than that in boys (18.3%, 20/109, χ²=12.171, P<0.05). There was no significant difference in the rate of positive diagnosis among all age groups (χ²=4.349, P>0.05). Interestingly, the scores of gross motors of positive group were significantly lower than that of negative group (61.5 vs. 69.4, t=-2.610, P<0.05). Otherwise, no significant difference was seen between two groups(t=-0.933, -1.298, -0.114, -0.214, all P>0.05). Conclusions: Language delay/disorder has complex genetic heterogeneity. WES has important application value in early etiological diagnosis for children with language delay/disorder.

Disparate Mutations in B-Acute Lymphoblastic Leukemia Among African American and European American Children

Background: B-acute lymphoblastic leukemia (B-ALL) is considered to be the most common malignancy diagnosed in childhood and leading cause of cancer-related death in children. There have been advances in the efficacy of multi-agent chemotherapy and stratification of treatment intensity according to clinical features of the patient, biologic features of leukemia cells, and early response to treatment. These advances herald the promise and challenges of precision medicine strategies that integrate leukemia genomics into contemporary therapy. Despite this progress, there are unmet needs related to the treatment of B-ALL. Among them the incidence varies according to race: African American (AA) children have significantly lower incidence of B-ALL compared to European American (EA). However, studies have shown that AA children have significantly lower survival rates compared to EA children. This disparity is not related to socioeconomic variables, suggesting a molecular basis for the lower survival rates of AA. Here we present a study showing race-specific genetic aberrations involved in leukemogenesis that may contribute to health disparities in B-ALL in AA and EA children.Aims: In a population of AA and EA pediatric B-ALL patients: 1) Discover the genomic susceptibility architecture at validated loci and determine whether genetic variants confer population-specific risks. 2) Define the landscape of molecular perturbation and genomic alterations. 3) Identify aberrant canonical pathways in leukemogenesis.Methods: A total of 20 newly diagnosed pediatric patients were utilized in our study (5 AA and 15 EA). Ages ranged between 1 and 18 years. Clinical history, hemogram, flow cytometry, immunophenotypic, morphologic, cytogenetic and prior molecular data were reviewed. None of the patients in our study had a relapse. Median percent cellularity present in the bone marrow aspirates was 100% (70% - 100%). Median percent of blasts was 94.8% (64.5% - 99.0%). Following manufacturer protocol (Qiagen, QIAmp DNA blood kit), 200µl of frozen bone marrow aspirates were used to extract the DNA. Following quality control on a Qubit fluorometer and RNA bioanalyzer, the samples were submitted to a translational genomics core for library preparation and whole-exome sequencing (TruSeq Exome, Illumina). Bioinformatics analysis was performed and genetic variants for each sample were identified.Results: We identified specific germ-line mutations within the most widely accepted cancer-related genes related to B-ALL. Most genetic aberrations (339) were shared between AA and EA, for example those present in the Anaplastic Lymphoma Receptor Tyrosine Kinase (ALK) gene. Some genes with genetic aberrations were specific of AA (58) such as, Lipoma Preferred Partner Gene (LPP) and others specific for EA (52) such as, Leukemia Inhibitory Factor Receptor (LIFR). The ingenuity pathway analysis revealed these genes clustered in race-specific canonical pathways. In AA, the specific pathways were related to telomerase signaling and cancer signaling. In EA, the specific pathways were related to stem cell pluripotency and hereditary cancers. Our findings suggest the value of whole exome sequencing as a tool for development of individual gene signatures and gene scores for AA and EA children afflicted by B-ALL.Conclusions: Overall, the prevalence of genetic aberrations in B-ALL may contribute to differences in incidences and outcomes between AA and EA children. Aberrant biological networks revealed by our study, provide information on distinguishing genetic aberrations and signaling networks that may be involved in race-specific leukemogenesis. Furthermore, our findings suggest that it may be possible to develop a whole-exome sequencing gene signature in B-ALL to help define a race-specific prognostic assay for B-ALL in bone marrow aspirates. In the future, the biomarker panel derived from this study will help guide risk stratification and treatments based on race and advance the prognosis of B-ALL in AA children. These findings may ultimately impact targeted disease management and contribute to the elimination of the disparate outcomes in B-ALL among AA children.Funding: Hyundai Hope on Wheels Scholar Grant, UMMC Division of Pediatric Hematology Oncology [Display omitted] DisclosuresNo relevant conflicts of interest to declare.