OBJECTIVE: To assess the diagnostic value of whole exome sequencing (WES) for patients with intellectual disability (ID) or global developmental delay (GDD). METHODS: 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). RESULTS: 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. CONCLUSION 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.
Humans ; Exome Sequencing ; Intellectual Disability/genetics* ; DNA Copy Number Variations ; Mutation ; Loss of Heterozygosity

OBJECTIVE: To detect loss of heterozygosity (LOH) at human leukocyte antigen (HLA) loci in a Chinese patient with leukemia after haploidentical hematopoietic stem cell transplantation. METHODS: HLA genotyping was carried out on peripheral blood, hair follicle and buccal swab samples derived from the patient after the transplantation as well as peripheral blood samples from his parents by using PCR-sequence specific oligonucleotide probe method and PCR-sequence based typing method. Short tandem repeat (STR) loci were detected by using a 23 site STR assay kit and a self-developed 6 STR loci assay for the HLA regions. RESULTS: After the transplantation, the HLA genotype of the peripheral blood sample of the patient was identical to his father. The patient was HLA-A*02:01,24:02, C*03:03,03:04, B*13:01,15:01, DRB1*08:03,12:02, DQB1*03:01,06:01 for his hair follicle specimen. However, homozygosity of the HLA loci was found in his buccal swab sample. Only the HLA-A*24:02-C*03:03-B*15:01-DRB1*08:03-DQB1*06:01 haplotype from his father's was present, while the HLA-A*02:01-C*03:04-B*13:01-DRB1*12:02-DQB1*03:01 haplotype from his mother was lost. After the transplantation, the alleles of the 23 STR sites in the patient's peripheral blood sample were consistent to his father, with no allelic loss detected in his buccal swab sample. However, at least 4 STR loci in the HLA region were lost in his buccal swab sample. CONCLUSION LOH at the HLA loci has been detected in the buccal swab sample of a patient with leukemia who received haploidentical hematopoietic stem cell transplantation.
HLA Antigens/genetics* ; HLA-A Antigens/genetics* ; Histocompatibility Antigens Class I/genetics* ; Humans ; Leukemia/genetics* ; Loss of Heterozygosity

OBJECTIVE: To assess the association of genomic instability of epithelial cadherin 1 (CDH1) gene and clinicopathological characteristics of gastric cancer. METHODS: In total 120 paraffin-embedded gastric cancer tissue specimen were prepared, and genomic DNA was extracted. The genomic instability of the CDH1 gene was analyzed by immunohistochemistry and silver staining PCR-single-strand conformation polymorphism. RESULTS: The number of information individuals (heterozygotes) was 98 for the D16S752 locus. The detection rates for microsatellite instability (MSI) and loss of heterozygosity (LOH) at the D16S752 locus and the positive rate of CDH1 protein were 19.39%, 16.33% and 51.02%, respectively. The detection rate of MSI in TNM stages I or II was significantly higher than that in stages III or IV (P<0.05) while the detection rate of LOH was significantly lower than that in stages III or IV (P<0.05). The positive rate of CDH1 protein in TNM stages III or IV was significantly lower than that in stages I or II (P<0.05). The detection rate of MSI of cases with lymph node metastasis was significantly lower than that of without lymph node metastasis (P<0.05) while the detection rate of LOH was significantly higher than that without lymph node metastasis (P<0.05). The positive rate of CDH1 protein in patients with lymph node metastasis was significantly lower than that in patients without lymph node metastasis (P<0.05). The positive rate of CDH1 protein in MSI-positive group was significantly higher than that in MSI-negative group (P<0.05), and the positive rate of CDH1 protein in the LOH-positive group was significantly lower than that the LOH-negative group (P<0.05). CONCLUSION The genomic instability of the CDH1 gene is associated with the progression of gastric cancer. MSI at the D16S752 locus may be used as a molecular marker for early gastric cancer, while LOH at this locus mostly occurs in advanced gastric cancer and can be regarded as an effective indicators for malignancy evaluation and prognosis.
Humans ; Stomach Neoplasms/pathology* ; Lymphatic Metastasis ; Cdh1 Proteins/genetics* ; Microsatellite Instability ; Loss of Heterozygosity ; Genomic Instability ; Microsatellite Repeats ; Antigens, CD/genetics* ; Cadherins/genetics*

OBJECTIVES: To observe and analyse the Amelogenin allelic loss in parent-child identification cases, and to explore the type and mechanism of Amelogenin allelic loss as well as its influence on gender identification and solutions. METHODS: After the detection by SiFaSTR™ 23plex DNA identification system, samples had the characteristics of the peak area of Amelogenin X was the same as the one of adjacent heterozygote or lower than one half of adjacent homozygote in females while Amelogenin X loss was observed in males were selected. X chromosome STR （X-STR） typing and Amelogenin X sequencing were performed. The samples with Amelogenin Y loss in males were confirmed by the detection of Y chromosome STR typing and sex-determining region of Y （SRY）. The type and rate of Amelogenin allelic loss were confirmed and calculated, and the mechanism and influence of this variation were also analysed. RESULTS: Amelogenin X allelic loss was observed in one male sample, the mutation in primer-binding region was confirmed by sequencing. The suspected Amelogenin X allelic loss was observed in four female samples, but the mutation in primer-binding region was confirmed by sequencing in only one sample. Amelogenin Y allelic loss was observed in seven male samples, SRY positive cases was detected in five of them, and two were SRY negative. Y-STR type was detected in four cases of the five SRY positive cases, which was not detected in the two SRY negative cases. The rate of Amelogenin allelic loss was about 0.029%. CONCLUSIONS Amelogenin X allelic loss does not affect the gender identification, but Amelogenin Y allelic loss may cause wrong gender identification. Thus, Y-STR or SRY should be detected for gender confirmation. When Y-STR genotypes are not detected in a "male" whose SRY detection is also negative, then the chromosome karyotype analysis and sex differentiation related genes test should be taken to further confirm the gender.
Amelogenin/genetics* ; DNA/genetics* ; Female ; Humans ; Loss of Heterozygosity/genetics* ; Male ; Sex Determination Analysis

OBJECTIVES: To analyse the genetic polymorphism of 21 autosome STR loci in Han population of Shandong Province and the cases with loci mutation or allelic loss typed by Goldeneye® DNA identification system 25A. METHODS: Totally 40 autosome STR loci types of 273 unrelated individuals in Han population of Shandong Province were typed by Goldeneye® DNA identification system 25A and 22NC, and the genetic polymorphism of 21 STR loci in those was analysed. Meanwhile, six cases with loci mutation were analysed by adding the tests with Goldeneye® DNA identification system 22NC, 20Y and 17X. Another three cases with allelic loss were tested by AmpFℓSTR® Identifiler® Plus PCR and analysed by gene sequencing. RESULTS: The genetic parameters of 21 autosome STR loci in Han population of Shandong Province were obtained. When STR loci were added up to 40, five of those with loci mutation met the identification requirements, and the results of X-STR or Y-STR types were consistent with that of STR loci. There was another duo case with one suspected loci mutation, biological source of six STR loci genotypes could not be found in the genotypes of supposed father. The Y-STR genotype of two individuals was identical that indicated both of them came from same paternal line. However, the fatherhood was excluded according to the autosome STR loci system. For two cases with allelic loss on D18S51, base mutation or loss were found in the primer binding domain of mother and child by gene sequencing. Another mother-child case with allelic loss on D13S317 was certified by AmpFℓSTR® Identifiler® Plus PCR kit. CONCLUSIONS The 21 autosome STR loci in Han population of Shandong Province have high polymorphism, which can be used in routine cases of paternity identification. For some duo cases with loci mutation, Goldeneye® DNA identification system 25A cannot satisfy the identification requirements, thus more autosome STR loci should be added properly. For the cases with allelic loss, the problem can be resolved by gene sequencing or using different merchant kits.
Asian People/genetics* ; China ; Gene Frequency ; Genetics, Population ; Genotype ; Humans ; Loss of Heterozygosity ; Microsatellite Repeats ; Mutation/genetics* ; Paternity ; Polymerase Chain Reaction ; Polymorphism, Genetic

No abstract available.
Aged ; Bone Marrow/pathology ; Genome, Human ; Humans ; Isochromosomes/*genetics ; Karyotyping ; Leukemia, Myeloid, Acute/complications/*diagnosis/genetics ; *Loss of Heterozygosity ; Male ; Oligonucleotide Array Sequence Analysis ; Thrombocytosis/*etiology

OBJECTIVETo verify the diagnosis of Angelman syndrome(AS) in a proband in order to provide prenatal diagnosis for his family.

METHODSArray comparative genome hybridization(array-CGH) and fluorescence in situ hybridization(FISH) on metaphase chromosomes were performed.

RESULTSThe karyotype of the proband was normal, and a regional deletion of 15q11.1-11.2 was detected by array-CGH. FISH analysis has confirmed loss of heterozygosity in 15q11.2. No positive results were obtained by array-CGH or karyotype analysis. Amniotic fluid sample was taken from the proband's mother upon her subsequent pregnancy. The karyotype of the fetus was normal, but SNP microarray chip analysis has identified loss of heterozygosity in 8p23.1-p22. As no abnormality was observed by ultrasound and other prenatal examinations, the pregnancy was recommended to continue to full-term, and a healthy infant was born.

CONCLUSIONClinically suspected AS can be diagnosed by array-CGH and FISH. The result may facilitate accurate genetic counseling and prenatal diagnosis for the affected family.

Adult ; Angelman Syndrome ; diagnosis ; genetics ; Chromosome Aberrations ; Chromosome Deletion ; Chromosomes, Human, Pair 15 ; genetics ; Chromosomes, Human, Pair 8 ; genetics ; Comparative Genomic Hybridization ; Female ; Fetal Diseases ; diagnosis ; genetics ; Humans ; In Situ Hybridization, Fluorescence ; Infant, Newborn ; Karyotyping ; Loss of Heterozygosity ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; Pregnancy ; Pregnancy Outcome ; Prenatal Diagnosis ; methods

We report three patients with normal karyotype (NK) ALL, who showed genetic aberrations as determined by high-resolution single nucleotide polymorphism array (SNP-A) analysis at both diagnosis and relapse. We evaluated the clinical relevance of the SNP-A assay for the detection of subtle changes in the size of affected genetic lesions at relapse as well as the prognostic value of the assay. In our patients, application of the SNP-A assay enabled sensitive detection of cryptic changes affecting clinically important genes in NK ALL. Therefore, this assay seems to be more advantageous compared to other conventional methods such as FISH assay, HemaVision (DNA Technology, Denmark), and conventional karyotyping for the detection of an "unstable genotype" at relapse, which may be associated with microscopic clonal evolution and poor prognosis. Further comprehensive studies are required to confirm the issues presented by our case patients in this report.
Adult ; Cyclin-Dependent Kinase Inhibitor p16/genetics ; Female ; Genotype ; Humans ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Loss of Heterozygosity ; Male ; Middle Aged ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*diagnosis/genetics ; Recurrence ; Retinoblastoma Protein/genetics

The combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH+SNP microarray) platform can simultaneously detect copy number alterations (CNA) and copy-neutral loss of heterozygosity (LOH). Eighteen children with acute myeloid leukemia (AML) (n=15) or myelodysplastic syndrome (MDS) (n=3) were studied using CGH+SNP microarray to evaluate the clinical significance of submicroscopic chromosomal aberrations. CGH+SNP microarray revealed CNAs at 14 regions in 9 patients, while metaphase cytogenetic (MC) analysis detected CNAs in 11 regions in 8 patients. Using CGH+SNP microarray, LOHs>10 Mb involving terminal regions or the whole chromosome were detected in 3 of 18 patients (17%). CGH+SNP microarray revealed cryptic LOHs with or without CNAs in 3 of 5 patients with normal karyotypes. CGH+SNP microarray detected additional cryptic CNAs (n=2) and LOHs (n=5) in 6 of 13 patients with abnormal MC. In total, 9 patients demonstrated additional aberrations, including CNAs (n=3) and/or LOHs (n=8). Three of 15 patients with AML and terminal LOH>10 Mb demonstrated a significantly inferior relapse-free survival rate (P=0.041). This study demonstrates that CGH+SNP microarray can simultaneously detect previously cryptic CNAs and LOH, which may demonstrate prognostic implications.
Adolescent ; Child ; Child, Preschool ; Chromosome Aberrations ; *Comparative Genomic Hybridization ; DNA/*analysis/metabolism ; DNA Copy Number Variations ; Female ; Hematopoietic Stem Cell Transplantation ; Humans ; Infant ; Kaplan-Meier Estimate ; Leukemia, Myeloid, Acute/*diagnosis/*genetics/therapy ; Loss of Heterozygosity ; Male ; Myelodysplastic Syndromes/*diagnosis/*genetics/therapy ; *Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Transplantation, Homologous

Carcinoma, Hepatocellular ; genetics ; pathology ; secondary ; Diagnosis, Differential ; Humans ; Liver Neoplasms ; genetics ; pathology ; secondary ; Loss of Heterozygosity ; Male ; Microsatellite Repeats ; Middle Aged ; Neoplasms, Multiple Primary ; genetics