Newborn Screening in Unselected Children Using Genomic Sequencing

Abstract Background: The aim of this study is to investigate potentially curable or treatable medical conditions in unselected newborns using genomic sequencing(GS). Methods: 321 newborns from a cohort of pregnant women from Qingdao, China, underwent high-depth GS (average 47.42 fold), with the approval of the ethics committee. 61 Mendelian Diseases, 151 Primary Immunodeficiency Diseases(PID) and 5 DPWG recommeded Essential pharmacogenetic(PGx) genes were analyzed. Results: 121 Mendelian pathogenic or likely pathogenic variants associated with 31 inherited diseases were detected, among these hearing loss, congenital hypothyroidism, methylmalonic acidemia, methylmalonic acidemia with homocystinuria, phenylketonuria(PKU) and benign hyperphenylalaninemia accounted for half of the carrier variants. Three children with compound heterozygous variants at GJB2 and PAH were confirmed by Sanger sequencing. Follow-up of the three families confirmed that one child was diagnosed with PKU and two children with GJB2 variants were scheduled to undergo hearing loss testing every six months after genetic counceling due to the nature of incomplete penetrance of hearing loss. 11 heterozygous pathogenic/ likely pathogenic variants in eight PID genes were identified in 11 infants. All 321 newborns carried at least one variant at the five DPGW recommended PGx genes. Codeine and clopidogrel require more attention in giving prescription for 25% and 8% of newborns have a decreased function of CYP2D6 and CYP2C19 enzymes respectively. Conclusions: Our study is the largest to date using GS to sequence unselected newborns. The results suggest that using GS may be a suitable method for screening newborns for variants in a large number of disease associated genes.

Download Full-text

A novel USH2A variant in a patient with hearing loss and prenatal diagnosis of a familial fetus: a case report

BMC Medical Genomics ◽

10.1186/s12920-021-01052-4 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Cong Zhou ◽

Yuanyuan Xiao ◽

Hanbing Xie ◽

Shanling Liu ◽

Jing Wang

Keyword(s):

Hearing Loss ◽

Prenatal Diagnosis ◽

Usher Syndrome ◽

Chinese Patient ◽

Compound Heterozygous ◽

Case Presentation ◽

Pathogenic Variants ◽

Compound Heterozygous Variants ◽

Gene Panels

Abstract Background Usher syndrome (USH) is the most common cause of inherited deaf-blindness. The current study aimed to identify pathogenic variants in a Chinese patient with hearing loss and to report the identification of a novel p.(Phe1583Leufs*10) variant in USH2A, which met the needs of prenatal diagnosis of the patient's mother. Case presentation Genomic DNA obtained from a five-year-old girl with hearing loss was analyzed via the hearing loss-targeted gene panels. We identified the compound heterozygous variants c.8559-2A>G and c.4749delT in Usher syndrome type 2A (USH2A) gene as the underlying cause of the patient; the former variation has been reported in the literature, but not the latter. The parents of the girl were heterozygous carriers. The two variants were classified as pathogenic. Based on these findings, amniotic fluid samples were used for prenatal diagnosis of the couple's fetus, which was found to carry c.4749delT but not c.8559-2A>G variation. During the follow-up period of more than 9 months after the birth of the fetus, it was confirmed that the infant was healthy. Conclusions The results of the present study identified two compound heterozygous USH2A variants in a patient with hearing loss and reported a novel USH2A variant which expands the spectrum of USH2A variants in USH.

Download Full-text

MO1027EFFICACY OF CALCINEURIN INHIBITORS IN CHILDREN WITH MONOGENIC STEROID-RESISTANT NEPHROTIC SYNDROME

Nephrology Dialysis Transplantation ◽

10.1093/ndt/gfab108.0024 ◽

2021 ◽

Vol 36 (Supplement_1) ◽

Author(s):

Larisa Prikhodina ◽

Svetlana Papizh ◽

Inna Povolotskaya

Keyword(s):

Nephrotic Syndrome ◽

Calcineurin Inhibitors ◽

Compound Heterozygous ◽

Target Level ◽

Steroid Resistant ◽

Steroid Resistant Nephrotic Syndrome ◽

Pathogenic Variants ◽

Nail Patella Syndrome

Abstract Background and Aims Monogenic causes of steroid-resistant nephrotic syndrome (SRNS) have been reported for up to one-third of children depending on age of the disease onset. Immunosuppressive treatment of genetic SRNS with calcineurin inhibitors (CNIs) is still controversial. The aim of the study was to investigate the efficacy of CNIs with focus on inducing remission and long-term kidney function in children with monogenic SRNS. Method Retrospective analysis of efficacy CNIs in five children (2M/3F) with monogenic SRNS was performed. Kidney biopsy prior CNIs revealed FSGS (n=4) and MCD (n=1). The initial cyclosporine (CsA) dose was 5 mg/kg/24h to keep a target level of 80-150 ng/ml and tacrolimus (TAC) - 0.1 mg/kg/24h to achieve a target level of 5-10 ng/ml. CsA took all 5 patients with subsequent switching to TAC in 2 children due to cosmetic side effects. The median follow-up period was 165.0 (IQR: 59.0; 185.5) months. Next generation sequencing (NGS) was used for identification of pathogenic variants in all patients. Results The median age at onset of monogenic SRNS was 33.0 (IQR: 16.5; 63.0) months. 2/5 (40%) patients presented with acute SRNS, 1/5 (20%) child with infantile NS, 1/5 (20%) - with isolated nephrotic range proteinuria with hypoalbuminemia and 1/5 (20%) - with NS and extrarenal features of Nail-Patella syndrome. NGS identified previously described pathogenic variants in all 5 children, including NPHS2 homozygous c.28dup (p.Glu87Ter) (n=1), NPHS2 compound heterozygous c.868G>A (p.Val290Met) in combination with c.686G>A (p.Arg229Gln) (n=1), LMX1B heterozygous c.788T>G (p.Val263Gly) (n=1), LMX1B heterozygous c.737G>A (p.Arg246Gln) (n=1), and COL4A3 heterozygous c.2962G>A (p.Gly988Arg) variant (n=1). The median time from diagnosis to initiation of CNIs treatment was 72.0 (IQR: 33.0; 93.0) months. CNIs induced complete remission in 2/5 (40%) patients, presented with acute SRNS, including one girl with MCD due to NPHS2 compound heterozygous variants with mutation-dependent pathogenicity of one (p.R229Q) of them and one boy with FSGS due to COL4A3 heterozygous variant (n=1). Partial remission was induced by CNIs in 2/5 (40%) girls with FSGS due to LMX1B heterozygous variants with isolated SRNS (n=1) and Nail-Patella syndrome (n=1). The median duration of CNIs treatment to obtain complete or partial remission was 13.5 (IQR: 6.8; 15.8) months. Acute CNIs-associated nephrotoxicity had 2 patients with LMX1B variants. At the last follow up full and partial responders to CNIs treatment aged of 16.5 (IQR: 11.8; 17.5) years had CKD-1 (n=3) and CKD-2 (n=1). 1/5 (20%) boy with NPHS2-associated infantile NS was CNI resistant and developed CKD-5 at the age of 6.5 years with subsequent living related kidney transplantation. Conclusion We found that 4/5 (80%) children with monogenic SRNS demonstrated partial or full response to CNIs treatment with stable long-term kidney function. We assume that CNIs might improve podocyte function by stabilization of their cytoskeleton disrupted in patients with monogenic SRNS.

Download Full-text

Novel compound heterozygous EYS variants may be associated with arRP in a large Chinese pedigree

Bioscience Reports ◽

10.1042/bsr20193443 ◽

2020 ◽

Vol 40 (6) ◽

Cited By ~ 1

Author(s):

Chunli Wei ◽

Ting Xiao ◽

Jingliang Cheng ◽

Jiewen Fu ◽

Qi Zhou ◽

...

Keyword(s):

Novel Mutation ◽

Gene Mutations ◽

Chinese Family ◽

Compound Heterozygous ◽

Missense Mutations ◽

The Novel ◽

Pathogenic Variants ◽

Pathogenic Genes ◽

Compound Heterozygous Variants ◽

Normal Controls

Abstract As a genetically heterogeneous ocular dystrophy, gene mutations with autosomal recessive retinitis pigmentosa (arRP) in patients have not been well described. We aimed to detect the disease-causing genes and variants in a Chinese arRP family. In the present study, a large Chinese pedigree consisting of 31 members including a proband and another two patients was recruited; clinical examinations were conducted; next-generation sequencing using a gene panel was used for identifying pathogenic genes, and Sanger sequencing was performed for verification of mutations. Novel compound heterozygous variants c.G2504A (p.C835Y) and c.G6557A (p.G2186E) for the EYS gene were identified, which co-segregated with the clinical RP phenotypes. Sequencing of 100 ethnically matched normal controls didn’t found these mutations in EYS. Therefore, our study identified pathogenic variants in EYS that may cause arRP in this Chinese family. This is the first study to reveal the novel mutation in the EYS gene (c.G2504A, p.C835Y), extending its mutation spectrum. Thus, the EYS c.G2504A (p.C835Y) and c.G6557A (p.G2186E) variants may be the disease-causing missense mutations for RP in this large arRP family. These findings should be helpful for molecular diagnosis, genetic counseling and clinical management of arRP disease.

Download Full-text

A novel LOXHD1 variant in a Chinese couple with hearing loss

Journal of International Medical Research ◽

10.1177/0300060519884197 ◽

2019 ◽

Vol 47 (12) ◽

pp. 6082-6090 ◽

Cited By ~ 1

Author(s):

Chuan Zhang ◽

Shengju Hao ◽

Yali Liu ◽

Bingbo Zhou ◽

Furong Liu ◽

...

Keyword(s):

Hearing Loss ◽

Molecular Diagnosis ◽

Protein Function ◽

Mexican American ◽

Compound Heterozygous ◽

Congenital Hearing Loss ◽

Targeted Next Generation Sequencing ◽

Novel Variants ◽

Novel Variant ◽

Compound Heterozygous Variants

Objective To perform molecular diagnosis and genetic counseling in a young Chinese couple with congenital hearing loss. Methods Variant screening analysis was performed by PCR and direct Sanger sequencing or targeted next-generation sequencing of all known hearing loss genes. Novel variants were evaluated by PolyPhen2 and PROVEAN software tools to evaluate possible effects on protein function. Results We identified causative variants in the young couple: c.235delC (rs80338943)/c.299-300delAT (rs111033204) compound heterozygous variants of GJB2 in the husband and c.1828G>A (p.Glu610Lys, rs535637788)/c.2825-2827delAGA compound heterozygous variants of LOXHD1 in the wife. The LOXHD1 c.1828G>A variant has only previously been reported in a Mexican-American individual in the 1000 Genomes Project database. Using PolyPhen2 and PROVEAN, we speculated that the LOXHD1 variant c.1828G>A is potentially pathogenic. Conclusion We carried out molecular diagnosis in a young couple with congenital hearing loss, and identified different disease-causing genes in the two individuals. The LOXHD1 variant c.1828G>A present in the wife had not previously been reported in individuals with congenital hearing loss. We determined this to be a potential pathogenic variant, and a novel variant associated with hearing loss in a Chinese individual.

Download Full-text

Clinical and Pathological Features of a Newborn With Compound Heterozygous ANKS6 Variants

Pediatric and Developmental Pathology ◽

10.1177/1093526619881541 ◽

2019 ◽

Vol 23 (3) ◽

pp. 235-239

Author(s):

Sakil Kulkarni ◽

Brooj Abro ◽

Maria Laura Duque Lasio ◽

Janis Stoll ◽

Dorothy K Grange ◽

...

Keyword(s):

Cardiac Failure ◽

Renal Dysplasia ◽

Cardiomyocyte Hypertrophy ◽

Compound Heterozygous ◽

Pathogenic Variants ◽

Whole Exome ◽

Genes Encoding ◽

Cystic Renal Dysplasia ◽

Cystic Renal Disease ◽

Compound Heterozygous Variants

We report a term female infant born to nonconsanguineous parents who presented with renal failure at birth, hypothyroidism, cholestasis, and progressive cardiac dysfunction. Multigene next-generation sequencing panels for cholestasis, cardiomyopathy, and cystic renal disease did not reveal a unifying diagnosis. Whole exome sequencing revealed compound heterozygous pathogenic variants in ANKS6 (Ankyrin Repeat and Sterile Alpha Motif Domain Containing 6), which encodes a protein that interacts with other proteins of the Inv compartment of cilium ( NEK8, NPHP2/INVS, and NPHP3). ANKS6 has been shown to be important for early renal development and cardiac looping in animal models. Autopsy revealed cystic renal dysplasia and cardiomyocyte hypertrophy, disarray, and focal necrosis. Liver histology revealed cholestasis and centrilobular necrosis, which was likely a result of progressive cardiac failure. This is the first report of compound heterozygous variants in ANKS6 leading to a nephronopthisis-related ciliopathy-like phenotype. We conclude that pathogenic variants in ANKS6 may present early in life with severe renal and cardiac failure, similar to subjects with variants in genes encoding other proteins in the Inv compartment of the cilium.

Download Full-text

Intragenic variants in the SMN1 gene determine the clinical phenotype in 5q spinal muscular atrophy

Neurology Genetics ◽

10.1212/nxg.0000000000000505 ◽

2020 ◽

Vol 6 (5) ◽

pp. e505

Author(s):

Rodrigo de Holanda Mendonça ◽

Ciro Matsui ◽

Graziela Jorge Polido ◽

André Macedo Serafim Silva ◽

Leslie Kulikowski ◽

...

Keyword(s):

Spinal Muscular Atrophy ◽

Copy Number ◽

Clinical Phenotype ◽

Muscular Atrophy ◽

Large Population ◽

Survival Motor Neuron ◽

Compound Heterozygous ◽

Pathogenic Variants ◽

Exon 1 ◽

Compound Heterozygous Variants

ObjectiveThe aim of the study was to report the proportion of homozygous and compound heterozygous variants in the survival motor neuron 1 (SMN1) gene in a large population of patients with spinal muscular atrophy (SMA) and to correlate the severity of the disease with the presence of specific intragenic variants in SMN1 and with the SMN2 copy number.MethodsFour hundred fifty Brazilian patients with SMA were included in a retrospective study, and clinical data were analyzed compared with genetic data; the SMN2 copy number was obtained by multiplex ligation-dependent probe amplification and pathogenic variants in SMN1 by next-generation sequencing.ResultsFour hundred two patients (89.3%) presented homozygous exon 7-SMN1 deletion, and 48 (10.7%) were compound heterozygous for the common deletion in one allele and a point mutation in the other allele. Recurrent variants in exons 3 and 6 (c.460C>T, c.770_780dup and c.734_735insC) accounted for almost 80% of compound heterozygous patients. Another recurrent pathogenic variant was c.5C>G at exon 1. Patients with c.770_780dup and c.734_735insC had a clinical phenotype correlated with SMN2 copy number, whereas the variants c.460C>T and c.5C>G determined a milder phenotype independently of the SMN2 copies.ConclusionsPatients with specific pathogenic variants (c.460C>T and c.5C>G) presented a milder phenotype, and the SMN2 copy number did not correlate with disease severity in this group.

Download Full-text

Audiological features in Serbian patients with hearing impairment identified with c.35delG in the GJB2 gene

Srpski arhiv za celokupno lekarstvo ◽

10.2298/sarh201117098d ◽

2021 ◽

pp. 98-98

Author(s):

Bojana Dobric ◽

Danijela Radivojevic ◽

Jovana Jecmenica ◽

Vassos Neocleous ◽

Pavlos Fanis ◽

...

Keyword(s):

Hearing Loss ◽

Hearing Impairment ◽

Autosomal Recessive ◽

Gjb2 Gene ◽

Compound Heterozygous ◽

Heterozygous State ◽

Phenotype Correlation ◽

Pathogenic Variants ◽

Environmental Causes ◽

35Delg Mutation

Introduction/Objective. Hearing impairment (HI) is the most common sensorineural disorder with an incidence of 1/700-1000 newborns. Variants in the GJB2 gene are the major cause of autosomal recessive nonsyndromic sensorineural hearing loss (ARNSHL). The degree of HI in patients with detected mutations in GJB2 gene ranges from mild to profound. The aim of this study was to determine possible genotype-phenotype association between audiometric characteristics and detected genotypes in ARNSHL patients from Serbia. Methods. Ninety-two patients with ARNSHL underwent genetic analysis with PCR-ARMS and sequencing of the GJB2 gene. Audiological analyses were obtained in all patients using a combination of several methods to estimate the degree of hearing loss. Results. Audiological analysis performed in the 92 probands showed moderate to profound range of hearing loss. All identified pathogenic variants accounted for 42.39% of the mutant alleles (78/184 alleles), with the c.35delG mutation being the most frequent (30.43%). Genotype-phenotype correlation in an isolated group of 37 patients bearing c.35delG in the homozygous, compound heterozygous or heterozygous state. In this group the majority of patients (30/37, 81.08%) exhibited severe to profound hearing deficit. Conclusion. Association between genotype and the degree of hearing impairment in patients analyzed in this study demonstrated that patients with bi-allelic truncating mutations i.e. c.35delG, associate with the more severe hearing loss when compared with those identified with only one affected allele. The various degrees of hearing impairment observed in heterozygous patients could be explained by the presence of an undetected second mutation or other modifier genes or environmental causes.

Download Full-text

Identification of Novel Compound Heterozygous MYO15A Mutations in Two Chinese Families with Autosomal Recessive Nonsyndromic Hearing Loss

Neural Plasticity ◽

10.1155/2021/9957712 ◽

2021 ◽

Vol 2021 ◽

pp. 1-9

Author(s):

Xiao-Hui Wang ◽

Le Xie ◽

Sen Chen ◽

Kai Xu ◽

Xue Bai ◽

...

Keyword(s):

Hearing Loss ◽

Autosomal Recessive ◽

Bioinformatics Analysis ◽

Compound Heterozygous ◽

Congenital Deafness ◽

Chinese Families ◽

Novel Variants ◽

Common Causes ◽

Compound Heterozygous Variants ◽

Generation Sequencing

Congenital deafness is one of the most common causes of disability in humans, and more than half of cases are caused by genetic factors. Mutations of the MYO15A gene are the third most common cause of hereditary hearing loss. Using next-generation sequencing combined with auditory tests, two novel compound heterozygous variants c.2802_2812del/c.5681T>C and c.5681T>C/c.6340G>A in the MYO15A gene were identified in probands from two irrelevant Chinese families. Auditory phenotypes of the probands are consistent with the previously reported for recessive variants in the MYO15A gene. The two novel variants, c.2802_2812del and c.5681T>C, were identified as deleterious mutations by bioinformatics analysis. Our findings extend the MYO15A gene mutation spectrum and provide more information for rapid and precise molecular diagnosis of congenital deafness.

Download Full-text

Novel HSD17B4 Variants Cause Progressive Leukodystrophy in Childhood: Case Report and Literature Review

Child Neurology Open ◽

10.1177/2329048x211048613 ◽

2021 ◽

Vol 8 ◽

pp. 2329048X2110486

Author(s):

Akiyo Yamamoto ◽

Shinobu Fukumura ◽

Yumi Habata ◽

Sachiko Miyamoto ◽

Mitsuko Nakashima ◽

...

Keyword(s):

Hearing Loss ◽

Brain Magnetic Resonance Imaging ◽

Compound Heterozygous ◽

Long Chain Fatty Acids ◽

Developmental Regression ◽

Whole Exome ◽

Uncertain Significance ◽

Compound Heterozygous Variants ◽

High Degree ◽

Moderate Hearing Loss

D-bifunctional protein (DBP) deficiency is a peroxisomal disorder with a high degree of phenotypic heterogeneity. Some patients with DBP deficiency develop progressive leukodystrophy in childhood. We report a 6-year-old boy with moderate hearing loss who presented with developmental regression. Brain magnetic resonance imaging demonstrated progressive leukodystrophy. However, very long chain fatty acids (VLCFAs) in the plasma were at normal levels. Whole-exome sequencing revealed compound heterozygous variants in HSD17B4 (NM_000414.3:c.[350A > T];[394C > T], p.[[Asp117Val]];[[Arg132Trp]]). The c.394C > T variant has been identified in patients with DBP deficiency and is classified as likely pathogenic, while the c.350A > T variant was novel and classified as uncertain significance. Although one of the two variants was classified as uncertain significance, an accumulation of phytanic and pristanic acids was identified in the patient, confirming type III DBP deficiency. DBP deficiency should be considered as a diagnosis in children with progressive leukodystrophy and hearing loss even if VLCFAs are within normal levels.

Download Full-text

Novel MFSD8 Variants in a Chinese Family with Nonsyndromic Macular Dystrophy

Journal of Ophthalmology ◽

10.1155/2021/6684045 ◽

2021 ◽

Vol 2021 ◽

pp. 1-5

Author(s):

Qin Xiang ◽

Yanna Cao ◽

Hongbo Xu ◽

Zhijian Yang ◽

Liang Tang ◽

...

Keyword(s):

Family Members ◽

Major Facilitator Superfamily ◽

Chinese Family ◽

Macular Dystrophy ◽

Compound Heterozygous ◽

The Novel ◽

Pathogenic Variants ◽

Compound Heterozygous Variants ◽

Major Facilitator ◽

Mfsd8 Gene

Purpose. To identify the molecular etiology of a Chinese family with nonsyndromic macular dystrophy. Methods. Ophthalmic examinations were performed, and genomic DNA was extracted from available family members. Whole exome sequencing of two members (the proband and her unaffected mother) and Sanger sequencing in available family members were performed to screen potential pathogenic variants. Results. Novel compound heterozygous variants, c.1066C>T (p.Pro356Ser) and c.1102+2T>C, in the major facilitator superfamily domain containing 8 gene (MFSD8) were suspected to be involved in this family’s macular dystrophy phenotype. The novel c.1066C>T variant in the MFSD8 gene probably resulted in substitution of serine for proline at the 356th residue and was predicted to be “uncertain significance” through in silico analyses. The novel c.1102+2T>C variant in the MFSD8 gene was likely to affect the splicing form and predicted to be “pathogenic.” Conclusion. The novel compound heterozygous variants, c.1066C>T (p.Pro356Ser) and c.1102+2T>C, in the MFSD8 gene are likely responsible for the isolated macular dystrophy phenotype in this family. This study enlarged the MFSD8 gene mutant spectrum and might provide more accurate genetic counseling for this family.

Download Full-text