OBJECTIVE: To explore the clinical features and genetic characteristics of three patients with Infantile liver failure syndrome type 2 (ILFS2). METHODS: Three children who were diagnosed with ILFS2 at the Children's Hospital Affiliated to Zhengzhou University from February 2023 to February 2024 were selected as the study subjects. Clinical data of the children were collected. Peripheral blood samples of the children and their parents were collected and subjected to whole exome sequencing (WES). Candidate variants of the NBAS gene were verified by Sanger sequencing. This study was approved by the Ethics Committee of the Children's Hospital Affiliated to Zhengzhou University (Ethics No. 2024-k-069). RESULTS: The three children had presented with fever-triggered recurrent acute liver failure. All of them were found to harbor compound heterozygous variants of the NBAS gene, including c.3596G>A and c.1181A>T in child 1, c.2617C>T and c.2T>C in child 2, and c.3596G>A and c.2817_2818insT in child 3. Among these, the c.1181A>T and c.2817_2818insT variants were unreported previously. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), they were respectively classified as variants of uncertain significance (PM2_Supporting+PM3+PP3) and pathogenic (PVS1+PM2_Supporting+PM3). CONCLUSION Combined with the patient's clinical phenotype, the compound heterozygous variants of the NBAS gene probably underlay the pathogenesis of ILFS2 in the three children. For children with fever-related acute liver failure of unknown causes, the possibility of this disease should be suspected, and genetic testing may facilitate the diagnosis. Early diagnosis and timely intervention can significantly improve the prognosis. Discoveries of the c.1181A>T and c.2817_2818insT variants have enriched the mutational spectrum of the NBAS gene.
Humans ; Exome Sequencing ; Genetic Testing/methods* ; Liver Failure, Acute/etiology* ; Mutation ; Child ; Adult ; Neoplasm Proteins

OBJECTIVE: To investigate the clinical features and genetic variants associated with Multiple mitochondrial dysfunction syndrome (MMDS) type 3 in two children. METHODS: Two children diagnosed with MMDS type 3 at Zhuhai Maternal and Child Health Care Hospital in January 2021 were selected for this study. A retrospective analysis of their clinical data was carried out. Whole exome sequencing was conducted on the two children and their parents, followed by Sanger sequencing for candidate variants and bioinformatic analysis. Both children received comprehensive rehabilitative therapy and were followed up for 3 years. This study was approved by the Ethics Committee of Zhuhai Maternal and Child Health Hospital (Ethics No. 202380). RESULTS: The two MMDS type 3 children were monozygotic twin girls, aged 9 months, presenting with developmental regression, pyramidal signs, and other clinical manifestations. Cranial MRI revealed widespread abnormal signals and vacuolar changes in the white matter. Whole exome sequencing revealed that both children had harbored compound heterozygous variants of the IBA57 gene, namely c.286T>C (p.Tyr96His) and c.307C>T (p.Gln103Ter). Sanger sequencing confirmed that these variants were inherited from their father and mother, respectively. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, both variants were classified as pathogenic (PM2_Supporting+PM3_Very Strong+PP3_Moderate; PVS1+PM2_Supporting+PM3). After treatment with vitamins, levocarnitine, ATP, coenzyme Q10, and other drugs, both children showed partial recovery of neurodevelopmental regression, with improvement in feeding and sleep. Over the 3-year follow-up, there was slow but progressive improvement in motor, language, and cognitive development. CONCLUSION The compound heterozygous variants c.286T>C (p.Tyr96His) and c.307C>T (p.Gln103Ter) of the IBA57 gene probably underlay the MMDS type 3 in the twin pair. Clinicians should be vigilant about the possibility of MMDS type 3 in children with neurodevelopmental regression and early cranial MRI findings indicating widespread white matter abnormalities with vacuolar changes, as these may be indicative of IBA57 gene variants.
Female ; Humans ; Infant ; Calcium-Binding Proteins/genetics* ; Exome Sequencing ; Genetic Testing/methods* ; Microfilament Proteins/genetics* ; Mitochondrial Diseases/genetics* ; Mutation ; Retrospective Studies ; Carrier Proteins

OBJECTIVE: To explore the genotype-phenotype correlation in a Charcot-Marie-Tooth type 2A2A (CMT2A2A) pedigree and to provide genetic counseling for its subsequent pregnancies. METHODS: A Chinese pedigree presenting with "lower limb muscle atrophy and movement disorders" at the Prenatal Diagnosis Center of Xuzhou Central Hospital between January and August 2024 was selected as the study subject. Relevant clinical data were collected from the pedigree members. Peripheral blood samples from affected individuals, and amniotic fluid and/or chorionic villus samples were obtained for DNA extraction. Whole exome sequencing (WES) was carried out. Candidate variants were verified by Sanger sequencing. Pathogenicity assessment and bioinformatic analysis were conducted. This study was approved by the Medical Ethics Committee of Xuzhou Central Hospital (Ethics No. XZXY-LK-20240111-0019). RESULTS: All affected individuals in this pedigree were females, whom included the proband, her mother, and her first daughter. Earlier age of onset was associated with more severe lower limb atrophy. A heterozygous missense variant of the MFN2 gene, namely c.314C>T (p.Thr105Met), was identified in the proband, her mother, daughter, and the third fetus from a re-marriage. The same variant was absent in her elder brother, current husband, and her fourth fetus. Based on the guidelines from American College of Medical Genetics and Genomics (ACMG) and recommendations from Clinical Genome Resources (ClinGen), the variant was classified as pathogenic (PP1_Strong+PM1+PS3+PS4_Moderate+PP3_Moderate+PM2_Supporting). Analyses with PROVEAN and Mutation Taster had categorized the variant as "deleterious" and "disease-causing", respectively. Analysis with Uniprot and Jalview showed that the affected amino acid residue is conserved across multiple species. ChEBI software predicted that the variant may alter the polarity of the 105th amino acid residue. CONCLUSION The c.314C>T (p.Thr105Met) missense variant of the MFN2 gene probably underlie the CMT2A2A in this pedigree. Above finding has enabled prenatal diagnosis and genetic counseling for its subsequent pregnancies.
Adult ; Female ; Humans ; Male ; Charcot-Marie-Tooth Disease/genetics* ; East Asian People/genetics* ; Exome Sequencing ; Genetic Testing/methods* ; GTP Phosphohydrolases/genetics* ; Mitochondrial Proteins/genetics* ; Mutation, Missense ; Pedigree

Next generation sequencing (NGS) technologies, including whole exome sequencing (WES) and whole genome sequencing (WGS), have greatly increased the diagnostic rates for genetic disorders. However, challenges still remain with the interpretation of variants of uncertain significance (VUS), variants in non-coding regions, and understanding of the effects of such variants on downstream genes. As a result, the diagnostic rates have typically ranged from 25% to 57%. RNA sequencing (RNA-seq) can complement DNA sequencing by revealing the functional consequences of genetic variants through the detection of aberrant gene expression, abnormal splicing events, allele-specific expression, and fusion gene expression. This has further increased the diagnostic rate of genetic disorders and enriched their therapeutic strategies. By broadening the scope of conventional genomic diagnostic methods, RNA-seq is poised to become a novel tool for the diagnosis of genetic disorders. This review has explored the methodologies and technical characteristics of RNA-seq by focusing on its recent advancement in clinical diagnosis, applications in undiagnosed genetic disorders, and the main challenges encountered.
Humans ; Genetic Diseases, Inborn/genetics* ; High-Throughput Nucleotide Sequencing/methods* ; Sequence Analysis, RNA/methods* ; Exome Sequencing/methods*

OBJECTIVE: To assess the diagnostic value of whole exome sequencing (WES) for fetuses undergone induced abortion due to structural abnormalities. METHODS: A retrospective analysis was carried out on 43 aborted fetuses with negative results for copy number variation (CNV) testing from January 2023 to June 2024 at Northwest Women's and Children's Hospital. Trio-WES was carried out on the tissues from the aborted fetuses. This study has been approved by the Ethics Committee of the Hospital (Ethics No. 21-036). RESULTS: Among the 43 abortic fetuses, WES has detected pathogenic variants in 15 cases, with a total of 9 pathogenic variants, 5 suspected pathogenic variants, and 5 variants of uncertain significance. No definite pathogenic variants were detected in the remaining 28 cases. CONCLUSION For fetuses with structural abnormalities and negative results from CNV testing, WES can increase the diagnostic rate and facilitate etiological diagnosis and genetic counseling.
Humans ; Female ; Exome Sequencing/methods* ; Pregnancy ; DNA Copy Number Variations/genetics* ; Retrospective Studies ; Adult ; Prenatal Diagnosis/methods* ; Abortion, Induced ; Fetus/abnormalities* ; Congenital Abnormalities/diagnosis* ; Genetic Testing ; Aborted Fetus/abnormalities*

OBJECTIVE: To assess the value of whole exome sequencing (WES) for the diagnosis of early-onset genetic diseases among infants aged 0 to 6 month in Ningbo region. METHODS: 268 infants presented at the Women and Children's Hospital Affiliated to Ningbo University from January 2022 to June 2024 undergoing WES-based genetic testing were enrolled. Peripheral blood samples were collected from the infants and their parents and subjected to WES. Pathogenic variants were identified by clinical manifestations. This study has been approved by the Medical Ethics Committee of the Hospital (Ethics No. EC2023-017). RESULTS: Among the 268 infants, 124 (46.3%) had phenotype-explaining genetic variants. For 42 family-based WES tests, 20 (47.62%) were abnormal, whilst in 226 single-person WES tests, 104 (46.02%) had abnormalities, with 76 (33.63%) verified by parental testing. In 96 fully family-verified cases, 31 were de novo, 40 were parent-inherited, 25 were single-parent-inherited. These included 35 inborn metabolic errors, 28 rare syndromes, 9 neurodevelopmental disorders, 4 musculoskeletal diseases, 5 congenital deafness, 2 mitochondrial diseases, 4 endocrine diseases, and 9 others. Among these, there were 7 pathogenic copy number variations (all deletions), 3 chromosomal abnormalities, and 85 single-nucleotide variations. One case of Beckwith-Wiedemann syndrome was detected by methylation MLPA. Among the single-nucleotide variants, 114 pathogenic/likely pathogenic variants were identified in 61 genes, with common ones including missense variants (64.04%), frameshifting variants (20.18%) and splicing variants (4.39%). CONCLUSION WES can offer effective diagnosis for hereditary diseases with specific/non-specific manifestations. For early-age infants, higher detection rates may be attained for inborn metabolic errors, rare syndromes, neurodevelopmental disorders, congenital deafness, and musculoskeletal diseases. Compared with single-person WES, family-based WES can attain a higher diagnostic efficiency.
Humans ; Exome Sequencing/methods* ; Infant ; Female ; Male ; Infant, Newborn ; Genetic Diseases, Inborn/diagnosis* ; Genetic Testing/methods*

OBJECTIVE: To explore the genetic etiology of fetal skeletal dysplasia using whole exome sequencing (WES) and copy number variation sequencing (CNV-seq) techniques, and the feasibility of using WES as the first-tier method for such fetuses. METHODS: Seventy four fetuses with skeletal dysplasia detected by prenatal ultrasound at the Genetic Testing Center of the Women and Children's Hospital Affiliated to Qingdao University from January 2020 to August 2024 were selected as the study subjects. Fetal muscle and peripheral blood samples of the pregnant women and their spouses were collected and subjected to WES analysis. CNV-seq was carried out on all fetal muscle tissue samples. And the results were compared with the CNVs indicated by WES. Genetic etiologies were analyzed across different subtypes of skeletal dysplasia. And the feasibility of using WES as the first-tier genetic test for similar fetuses was assessed, in addition with a systematic cost-effectiveness analysis. This study was approved by the Medical Ethics Committee of the Hospital (Ethics No.: QFELL-YJ-2024-201). RESULTS: A total of 50 fetuses were diagnosed, which yielded a diagnostic rate of 67.57%. These included 6 chromosomal aneuploidies, 4 chromosomal CNVs and 40 monogenic disorders. The monogenic diseases had involved 46 variant sites in 23 pathogenic genes, among which 12 were unreported previously, including MYH3: c.735T>C, ALPL: c.1324C>T, NEK9: c.1973G>A, MAGEL2: c.2024_2025del, LMBR1: c.423+4914A>C, NEB: c.21273_21276del, COL1A1: c.2651G>C and c.2758G>C, ASPM: c.2473delinsGA, TBX5: c.704G>A, DYNC2H1: c.10893del, and DYNC2I2: c.1270C>T. Substantial concordance was reached between WES-derived CNV calls and CNV-seq findings. No clinically significant CNV was exclusively detected by CNV-seq. Cost-effectiveness modeling demonstrated that implementing WES as the first-tier genetic testing method could reduce the total expenditure when WES unit cost remained below 6.4 folds that of the CNV-seq. CONCLUSION Genetic variants including single nucleotide variations (SNV) of monogenic disorders, chromosomal aneuploidies and genomic CNVs are important causes for fetal skeletal dysplasia. WES is an accurate and efficient method for analyzing the etiology of fetal skeletal dysplasia, particularly in those with a family history of similar phenotype or maternal history of adverse pregnancies.
Humans ; Exome Sequencing/methods* ; Female ; Pregnancy ; DNA Copy Number Variations/genetics* ; Genetic Testing/methods* ; Prenatal Diagnosis/methods* ; Adult ; Male ; Fetus ; Bone Diseases, Developmental/diagnosis* ; Ultrasonography, Prenatal

As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits, a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data, sample quality issues, such as gender mismatch, abnormal inbreeding coefficient, cryptic relatedness, and population outliers, can also have fundamental impact on downstream analysis. However, there is a lack of tools specialized in identifying problematic samples from NGS data, often due to the limitation of sample size and variant counts. We developed SeqSQC, a Bioconductor package, to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access, and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor.org/packages/SeqSQC.
Breast Neoplasms ; genetics ; Cohort Studies ; Continental Population Groups ; genetics ; Female ; Genome, Human ; High-Throughput Nucleotide Sequencing ; methods ; standards ; Humans ; Software ; Whole Exome Sequencing

OBJECTIVETo explore the clinical and genetic features of a Chinese boy with oculocutaneous albinism.

METHODSThe clinical features of the patient were analyzed. The DNA of the patient and his parents was extracted and sequenced by next generation exome capture sequencing. The nature and impact of detected mutation were predicted and validated.

RESULTSThe child has displayed strabismus, poor vision, nystagmus and brown hair. DNA sequencing showed that the patient has carried compound heterozygous mutations of the TYRP1 gene, namely c.1214C>A (p.T405N) and c.1333dupG, which were inherited from his mother and father, respectively. Neither mutation was reported previously.

CONCLUSIONThe child has suffered from oculocutaneous albinism type Ⅲ caused by mutations of the TYRP1 gene.

Albinism, Oculocutaneous ; diagnosis ; genetics ; Amino Acid Sequence ; Base Sequence ; Child, Preschool ; Exome ; genetics ; Family Health ; Female ; Heterozygote ; High-Throughput Nucleotide Sequencing ; methods ; Humans ; Male ; Membrane Glycoproteins ; genetics ; Mutation ; Oxidoreductases ; genetics ; Parents

OBJECTIVETo detect potential mutation of NFU1 gene in a Chinese family affected with multiple mitochondrial dysfunction syndrome (MMDS).

METHODSFor a mother with two children died of MMDS, next-generation sequencing (NGS) was used to scan her exome. Suspected mutation was validated with PCR and Sanger sequencing. Potential mutation of exons 1 to 8 and flanking regions of the NFU1 gene was also detected in the father by PCR and Sanger sequencing.

RESULTSA novel deletional mutation c.90delC(p.Tyr30Ter) of the NFU1 gene was found in the mother, while the father was found to have carried a heterozygous c.572A>T (p.Asp191Val) mutation. The same mutations were not found among 100 healthy controls.

CONCLUSIONThe novel mutations c.90delC (p.Tyr30Ter) and c.572A>T (p.Asp191Val) of the NFU1 gene probably underlie the pathogenesis of MMDS in our case. Combined NGS and Sanger sequencing may provide efficient and accurate diagnosis for this disease.

Asian Continental Ancestry Group ; genetics ; Base Sequence ; Carrier Proteins ; genetics ; China ; Exome ; genetics ; Family Health ; Fatal Outcome ; Female ; Genetic Predisposition to Disease ; ethnology ; genetics ; Heterozygote ; High-Throughput Nucleotide Sequencing ; methods ; Humans ; Infant ; Male ; Mitochondrial Diseases ; ethnology ; genetics ; Mutation ; Pedigree ; Sequence Deletion ; Sequence Homology, Nucleic Acid