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 explore the molecular cytogenetic characteristics of three fetuses with psu idic(Y)(q11.22) using a combination of multiple methods. METHODS: A total of 11 000 pregnant women who underwent prenatal diagnosis at the Prenatal Diagnosis Center of Taizhou City from January 2019 to October 2024 were selected as the study subjects. Chromosome karyotype analysis (G-banding) and copy number variation analysis based on next-generation sequencing (NGS) were performed on the amniotic fluid/cord blood samples of the 11 000 fetuses. For cases suspected of Y chromosome abnormalities, C-banding and/or fluorescence in situ hybridization (FISH) and AZF microdeletion testing were additionally conducted. This study has been reviewed and approved by the Medical Ethics Committee of Taizhou Hospital, Zhejiang Province (Ethics No. KL20240860). RESULTS: Among the 11,000 prenatal samples undergoing concurrent karyotype and copy number variation analysis, two fetuses with 45,X/46,X,psu idic(Y)(q11.22) mosaicism and one fetus with 46,X,psu idic(Y)(q11.22) were detected. FISH detection indicated that approximately 66.7% of the cells in fetus 2 exhibited a dicentric Y chromosome, and the metaphase karyotype supported the presence of a pseudodicentric chromosome. AZF testing revealed complete deletion of the AZFb+AZFc regions in fetus 2 and fetus 3. CONCLUSION Conventional G-banding karyotype analysis for psu idic(Y)(q11.22) is prone to misdiagnosis or missed diagnosis. The combined application of chromosome karyotype analysis (G+C banding), copy number variation analysis, and FISH detection in clinical practice can accurately diagnose fetuses with psu idic(Y).
Humans ; Female ; Pregnancy ; Prenatal Diagnosis/methods* ; DNA Copy Number Variations/genetics* ; Adult ; Chromosomes, Human, Y/genetics* ; Karyotyping ; In Situ Hybridization, Fluorescence ; Cytogenetic Analysis/methods* ; Fetus ; High-Throughput Nucleotide Sequencing ; Male

OBJECTIVE: To provide preimplantation genetic testing (PGT) for a patient with Incontinentia pigmenti (IP) due to IKBKG gene variant but without family samples through construction of single nucleotide polymorphism (SNP)-based haplotype by Long-read sequencing (LRS) technology. METHODS: A female IP patient with a heterozygous IKBKG c.1167dup variant but without family genetic data who sought genetic counseling at Women and Children' Hospital of Ningbo University in November 2021 was selected as the study subject. The IKBKG gene has a highly homologous pseudogene IKBKGP1. Genomic DNA was extracted from peripheral blood samples from the couple, and LRS was used to obtain informative SNP loci flanking the variant locus, enabling the construction of SNP haplotype with a long segment spanning from the non-homologous region of IKBKG to the variant site. Trophoblast cells were biopsied from blastocysts fertilized through intracytoplasmic sperm injection, and next-generation sequencing (NGS) was used to determine the SNP information of the embryos. Linkage analysis with the parental SNP haplotypes was conducted to detect the carrier status of the embryos and exclude chromosomal aneuploidies. Sanger sequencing was carried out to validate the result. A euploid embryo without the pathogenic variant was selected for transfer. Prenatal diagnosis was carried out by amniocentesis at mid-trimester to verify the result of PGT tests, and follow-up was conducted after the baby was born. This study has been approved by the Ethics Committee of Women and Children's Hospital of Ningbo University (Ethics No. EC2023-094). RESULTS: A total of seven blastocysts were tested, and PGT results indicated that two embryos were euploid and did not carry the pathogenic variant. One euploid embryo was transferred, which resulted in a singleton pregnancy. Amniocentesis at 24 weeks of gestation confirmed that the status of fetal IKBKG gene, and its chromosomal status was consistent with the PGT results. A healthy male infant was born at 38+6 weeks of gestation. CONCLUSION For IP patients with de novo mutation or without family genetic samples, PGT with LRS can directly construct the SNP-based haplotype while avoiding interference from pseudogenes, providing an effective strategy for PGT.
Female ; Humans ; Male ; Pregnancy ; Genetic Testing/methods* ; Haplotypes/genetics* ; High-Throughput Nucleotide Sequencing/methods* ; I-kappa B Kinase/genetics* ; Incontinentia Pigmenti/diagnosis* ; Polymorphism, Single Nucleotide/genetics* ; Preimplantation Diagnosis/methods* ; Infant, Newborn

OBJECTIVE: To analyze the carrier rates and profiles of pathogenic and likely pathogenic variants for hearing loss-related genes MYO7A, PCDH15, and CDH23 among neonates in Nanjing city through targeted next-generation sequencing (NGS). METHODS: Heel-prick blood samples were collected from 30 043 newborns delivered at Nanjing Women and Children's Health Care Hospital between March 2022 and April 2024. Dried blood spots were prepared, and genomic DNA was extracted. Targeted NGS was applied to detect variants across the full coding regions of the MYO7A, PCDH15, and CDH23 genes. The carrier rates and profiles of pathogenic and likely pathogenic variants of the three genes were analyzed. This study was approved by the Medical Ethics Committee of Nanjing Maternal and Child Health Care Hospital (Ethics No.: 2021KY-071). RESULTS: The carrier rates of pathogenic and likely pathogenic variants (with ≥ 1 variant site) for the MYO7A, PCDH15, and CDH23 genes were 0.340%, 0.226%, and 0.156%, respectively. A total of 65, 49, and 30 variant types were detected in the MYO7A, PCDH15, and CDH23 genes, respectively. For MYO7A, single base variants were predominant, with the most common variant being c.5581C>T, followed by c.1343+1G>A, c.2837T>G, and c.5660C>T, with allelic frequencies of 0.013% (8/60 086), 0.007% (4/60 086), 0.007% (4/60 086), and 0.007% (4/60 086), respectively. PCDH15 variants were mainly deletions, with the most common variant site being c.4699_4715dupAGAGAAAAGATTCAGAG, followed by c.3441delA, c.440T>G, and c.4733_4736delTCAG, with allelic frequencies of 0.015% (9/60 086), 0.005% (3/60 086), 0.005% (3/60 086), and 0.005% (3/60 086), respectively. For CDH23, single base variants were predominant, with c.6604G>A being the most common, followed by c.6085C>T, c.6050+9G>A, and c.6253+1G>A, with allelic frequencies of 0.013% (8/60 086), 0.012% (7/60 086), 0.005% (3/60 086), and 0.005% (3/60 086). CONCLUSION This study analyzed the carrier rates and profiles of pathogenic and likely pathogenic variants of the MYO7A, PCDH15, and CDH23 genes, which can provide more evidence for the prevention and management of deafness in the region.
Humans ; Cadherins/genetics* ; High-Throughput Nucleotide Sequencing/methods* ; Infant, Newborn ; Female ; Myosin VIIa/genetics* ; Cadherin Related Proteins ; Male ; Hearing Loss/genetics* ; Myosins/genetics* ; Heterozygote

OBJECTIVE: The haplotypes of Killer cell immunoglobulin-like receptors (KIR) can be divided into centromeric and telomeric ones. As the terminal gene at the centromeric end, KIR3DP1 plays an important role in stabilizing the haplotype structure. This study aimed to analyze the distribution of KIR3DP1 gene haplotypes among Han Chinese population in Zhejiang in order provide a basis for further analyzing the role of KIR3DP1 in the KIR haplotypes. METHODS: A total of 166 unrelated blood donors from Zhejiang were collected (Blood donation period: March 2020 to August 2020), and genotyping was performed by next-generation sequencing based on exon capture. The copy number and allelic frequency of the KIR3DP1 gene and the distribution of centromeric haplotypes were statistically analyzed. This study was approved by the Medical Ethics Committee of Zhejiang Blood Center (Ethics No.: 2023-001). RESULTS: The KIR3DP1 gene was positive for all individuals but with different copy numbers. Among these, 4 cases (2.4%) had only 1 copy, 156 cases (94.0%) had 2 copies, and 6 cases (3.6%) had 3 copies. A total of 10 KIR3DP1 alleles were found in the population, which could be classified into the KIR3DP1*001-L type, KIR3DP1*003-L type, and KIR3DP1 full deletion type. The KIR3DP1*003 L type allele was linked to the Cen-A01 and Cen-B01 types, and the KIR3DP1*001*L type allele and the KIR3DP1 deletion type were only present in the Cen-B02 type haplotype. CONCLUSION This study has derived a high-resolution distribution map of the KIR3DP1 gene in the Han population from Zhejiang, and found that the KIR3DP1 alleles showed different linkage with the centromeric haplotypes, which has provided a basis for further studying the role of KIR3DP1 in genetic immunity.
Adult ; Female ; Humans ; Male ; Alleles ; China/ethnology* ; Gene Frequency ; Genotype ; Haplotypes/genetics* ; High-Throughput Nucleotide Sequencing/methods* ; East Asian People/genetics* ; Receptors, KIR/genetics*

OBJECTIVE: To assess the value of combined detection strategies using multiple technologies for the genetic testing and prenatal diagnosis for pedigrees affected with Duchenne muscular dystrophy (DMD) for optimizing genetic counseling and reproductive guidance. METHODS: This study has involved 142 subjects from 65 suspected DMD families who had visited the First Affiliated Hospital of Chongqing Medical University from January 2018 to December 2023. A combination of multiple ligation-dependent probe amplification (MLPA), quantitative fluorescence PCR, and next-generation sequencing (NGS) was used. After confirming the genetic diagnosis of the probands, prenatal diagnosis was provided for carrier mothers. This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: 2021-264). RESULTS: Among the 142 subjects tested, 73 cases of large deletions/duplications and 15 cases of small variants of the DMD gene were detected. The hotspot regions for the variants were exons 45 to 55. A total of 41 variant types were identified, of which 3 were previously unreported. In 19 families with suspected patients, 7 exonic deletions, 2 exonic duplications, and 3 small variants were identified. Prenatal diagnosis was performed on 48 fetuses from 46 families, revealing 16 affected male fetuses (including 12 with deletion variants, 2 with duplication variants, and 2 with small variants). Seven carrier females were identified among the 16 female fetuses (including 6 with deletions and 1 with duplication). Among the couples with an affected fetus, 16 had opted to terminate the pregnancy, while the parents of 32 fetuses had chosen to continue with the pregnancy. In families undergoing prenatal diagnosis, 53 (79.1%) pregnant women and their family members were found to carry mutations of the DMD gene. CONCLUSION The combined detection strategy of MLPA, qPCR, and NGS can encompass large deletions/duplications and small variants of the DMD gene, providing timely and accurate prenatal diagnosis for families affected by DMD. In conjunction with genetic counseling, this can effectively reduce the risk of producing affected offspring, which is crucial for the prevention and control of this disease.
Humans ; Muscular Dystrophy, Duchenne/diagnosis* ; Prenatal Diagnosis/methods* ; Female ; Male ; Pregnancy ; Pedigree ; Genetic Testing/methods* ; Dystrophin/genetics* ; Adult ; Genetic Counseling ; High-Throughput Nucleotide Sequencing/methods* ; Exons

OBJECTIVE: To investigate the characteristics of chromosomal abnormalities in amniotic fluid among pregnant women in Liangshan Prefecture and explore strategies for optimizing prenatal diagnosis. METHODS: A retrospective analysis was conducted on 1 024 amniocentesis samples collected at the Prenatal Diagnosis Center of Liangshan Prefecture Maternal and Child Health Care Hospital between February 2022 and December 2024. Chromosome karyotyping analysis (3 cases had failed culture, 1 021 valid samples) was combined with high-throughput chromosome sequencing analysis (CNV-seq) for the detection. This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: 2023-07). RESULTS: The overall detection rate of chromosomal karyotype abnormalities in the amniotic fluid cells was 4.02% (41/1 021), with numerical abnormalities accounting for 80.49% (33/41) and structural abnormalities for 19.51% (8/41). Numerical abnormalities were primarily trisomy 21 (16/41, 39.02%) and 47,XXY (6/41, 14.63%). Structural abnormalities included translocations (6 cases) and mosaicism (2 cases). CNV-seq detected 22 pathogenic or likely pathogenic copy number variations, whilst the undetection rate for balanced translocations reached 100% (7/7). The combined application of karyotyping and CNV-seq, leveraging complementary strengths, can enhance the overall detection rate. CONCLUSION The distribution characteristics of chromosomal abnormalities in amniotic fluid from pregnant women in Liangshan exhibit regional specificity. A combined testing strategy significantly optimizes prenatal diagnosis efficacy, providing crucial evidence for enhancing the effectiveness of prenatal diagnosis in ethnic minority regions.
Humans ; Female ; Pregnancy ; Prenatal Diagnosis/methods* ; Chromosome Aberrations ; Retrospective Studies ; Adult ; Amniotic Fluid ; Karyotyping ; Amniocentesis ; Chromosome Disorders/genetics* ; China ; High-Throughput Nucleotide Sequencing ; DNA Copy Number Variations/genetics*

Objective To precisely identify the para-Bombay blood types in cancer patients at our hospital, establish a robust system for the identification of challenging blood types in our laboratory, and provide a foundation for precise transfusion practices. Methods We retrospectively analyzed the blood type results of 91 874 cancer patients from January 1, 2019, to December 31, 2023. Conventional serological methods were used to screen for blood types, and suspected para-Bombay blood types were identified. Further analysis was performed using Pacific Biosciences (PacBio) single-molecule real-time sequencing and Sanger sequencing was used to determine the genotypes of the ABO, FUT1, and FUT2 genes. Results Eight cases of para-Bombay blood type were confirmed through serological and molecular biological methods. The FUT1 genotypes identified were: 5 cases of h1h1 (homozygous mutation 551_552delAG) and 3 cases of h1h2 (compound heterozygous mutations of 551_552delAG and 880_882delTT). The FUT2 genotypes identified were: 2 cases of Se³⁵⁷/Se^{357, 716} and 4 cases of Se³⁵⁷/Se³⁵⁷. Additionally, one sample revealed a novel heterozygous mutation, 818C>T, in exon 7 of the ABO gene, which was confirmed by PacBio sequencing to be located on the O haplotype. Conclusion PacBio sequencing technology demonstrates significant advantages in analyzing the haplotypes of para-Bombay blood type genes. This approach supports the establishment of a robust system for the identification of challenging blood types and provides novel evidence for precise transfusion practices in cancer patients.
Humans ; Neoplasms/genetics* ; Fucosyltransferases/genetics* ; ABO Blood-Group System/genetics* ; Male ; High-Throughput Nucleotide Sequencing/methods* ; Galactoside 2-alpha-L-fucosyltransferase ; Female ; Retrospective Studies ; Genotype ; Middle Aged ; Blood Grouping and Crossmatching/methods* ; Adult ; Mutation ; Aged

This article reports the clinical characteristics and treatment processes of three cases of mucormycosis occurring after hematopoietic stem cell transplantation in children, along with a review of relevant literature. All three patients presented with chest pain as the initial symptom, and metagenomic next-generation sequencing (mNGS) confirmed the mucycete infection early in all cases. Two patients recovered after treatment, while one succumbed to disseminated infection. mNGS has facilitated early diagnosis and treatment, reducing mortality rates. Additionally, surgical intervention is an important strategy for improving the prognosis of this condition.
Humans ; Hematopoietic Stem Cell Transplantation/adverse effects* ; Mucormycosis/etiology* ; Male ; High-Throughput Nucleotide Sequencing/methods* ; Child ; Female ; Metagenomics ; Child, Preschool

OBJECTIVES: To evaluate the clinical value of next-generation sequencing (NGS) in neonatal disease screening, particularly its advantages when combined with tandem mass spectrometry (MS/MS). METHODS: A prospective study was conducted involving blood samples from 1 999 neonates born at the Shenzhen Guangming District People's Hospital, between May and August 2021. All samples were initially screened using MS/MS and fluorescence immunoassay, followed by NGS to detect high-frequency variation sites in 135 related pathogenic genes. Suspected positive variants were validated using Sanger sequencing or multiplex ligation-dependent probe amplification in family studies. RESULTS: No confirmed positive cases were found in the MS/MS analysis of the 1 999 neonates. Genetic screening identified 58 positive cases (2.90%), 732 carriers of pathogenic genes (36.62%), and 1 209 negative cases (60.48%). One case of neonatal intrahepatic cholestasis was diagnosed (0.05%, 1/1 999). Fluorescence immunoassay identified 39 cases of glucose-6-phosphate dehydrogenase (G6PD) deficiency (1.95%, 39/1 999), while genetic screening identified 43 cases of G6PD deficiency (2.15%, 43/1 999). The fluorescence immunoassay also detected 6 cases of hyperthyrotropinemia (0.30%, 6/1 999), all of whom carried DUOX2 gene variants. The top ten pathogenic gene carrier rates were G6PD (12.8%), DUOX2 (8.7%), HBB (8.2%), ATP7B (6.6%), GJB2 (5.7%), SLC26A4 (5.6%), PAH (5.6%), ACADSB (4.6%), SLC25A13 (4.2%), and SLC22A5 (4.1%). CONCLUSIONS NGS can serve as an effective complement to MS/MS, significantly improving the detection rate of inherited metabolic disorders in neonates. When combined with family validation, it enables precise diagnosis, particularly demonstrating complementary advantages in screening for monogenic diseases such as G6PD deficiency.
Humans ; Infant, Newborn ; High-Throughput Nucleotide Sequencing/methods* ; Neonatal Screening/methods* ; Tandem Mass Spectrometry ; Prospective Studies ; Female ; Male ; Infant, Newborn, Diseases/diagnosis* ; Genetic Testing