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 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*

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

Adenocarcinoma is the major histology of gallbladder cancer. There are three subtypes of adenocarcinoma of the gallbladder: biliary, intestinal, and gastric foveolar subtypes. Also, there are three premalignant lesions of gallbladder adenocarcinoma: adenoma, biliary intraepithelial neoplasia (BilIN), and intracystic papillary neoplasm (ICPN). Premalignant lesion is hyperplasia of dysplastic epithelial cells with no evidence of stromal invasion. BilIN is invisible in gross inspection but can be microscopically identified around invasive tumor or chronic cholecystitis. ICPN is grossly identified as exophytic polypoid mass or diffuse friable thickening of mucosa and composed of mucinous epithelial cells with papillary and tubular arrangement. Dysplasia of BilIN and ICPN is classified by using a three-tiered system and high grade dysplasia is the same group with carcinoma in situ. Adenoma and ICPN have some ambiguities in definition and re-establishment of diagnostic criteria is needed for reproducibility of diagnosis. KRAS, TP53, and CDKN2A are the representative altered molecules in gallbladder cancer. Molecular alteration during dysplasia-carcinoma sequence is too heterogenous depending to the risk factors and type of premalignant lesion to explain the whole process by single process. Over-expression of COX2, mutation of TP53, impairment of mitochondrial DNA were reported in early hyperplastic or metaplastic epithelium. Loss of heterozygosity (LOH) of 3p, 8p chromosomes and amplification of HER2 were reported in low grade dysplasia and LOH of 9p, 18q, 22q, 17p chromosomes and mutation of CDK2A were reported in high grade dysplasia/carcinoma in situ.
Adenocarcinoma ; Adenoma ; Bile Pigments ; Carcinogenesis ; Carcinoma in Situ ; Cholecystitis ; Diagnosis ; DNA, Mitochondrial ; Epithelial Cells ; Epithelium ; Gallbladder Neoplasms ; Gallbladder ; Hyperplasia ; Loss of Heterozygosity ; Mucins ; Mucous Membrane ; Precancerous Conditions ; Risk Factors

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

The concept of mosaicism has been used to explain different cutaneous patterns, such as the lines of Blaschko, the checkerboard pattern, the phylloid pattern, and a patchy pattern. Many mosaic patterns are caused by loss of heterozygosity, the genetic mechanism by which a heterozygous somatic cell becomes either homozygous or hemizygous. A particular form of loss of heterozygosity is twin spotting, which give rise to two contrary homozygous daughter cells. The concept of twin spotting has been used for some of these human phenotypes, which are characterized by the co-occurrence of two different nevi, including nevus vascularis mixtus. Nevus vascularis mixtus is a rare vascular malformation characterized by the coexistence of a nevus anemicus and a nevus telangiectaticus, and can be associated with extra-cutaneous anomalies, such as cerebral malformations. Herein, we report a 6-year-old girl with paired cutaneous vascular nevi telangiectaticus, anemicus, and nevus vascularis mixtus, that were distributed on the left side of her chest and left arm, without other systemic and neurologic anomalies.
Arm ; Child ; Female ; Humans ; Loss of Heterozygosity ; Metrorrhagia ; Mosaicism ; Nevus* ; Nuclear Family ; Phenotype ; Thorax ; Twins ; Vascular Malformations

BACKGROUND: Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a rare inherited disorder characterized by infantile-onset macrocephaly, slow neurologic deterioration, and seizures. Mutations in the causative gene, MLC1, are found in approximately 75% of patients and are inherited in an autosomal recessive manner. We analyzed MLC1 mutations in five unrelated Korean patients with MLC. METHODS: Direct Sanger sequencing was used to identify MLC1 mutations. A founder effect of the p.Ala275Asp variant was demonstrated by haplotype analysis using single-nucleotide polymorphic (SNP) markers. Multiple ligation-dependent probe amplification (MLPA) and comparative genomic hybridization plus SNP array were used to detect exonic deletions or uniparental disomy (UPD). RESULTS: The most prevalent pathogenic variant was c.824C>A (p.Ala275Asp) found in 7/10 (70%) alleles. Two pathogenic frameshift variants were found: c.135delC (p.Cys46Alafs*12) and c.337_353delinsG (p.Ile113Glyfs*4). Haplotype analysis suggested that the Korean patients with MLC harbored a founder mutation in p.Ala275Asp. The p.(Ile113Glyfs*4) was identified in a homozygous state, and a family study revealed that only the mother was heterozygous for this variant. Further analysis of MLPA and SNP arrays for this patient demonstrated loss of heterozygosity of chromosome 22 without any deletion, indicating UPD. The maternal origin of both chromosomes 22 was demonstrated by haplotype analysis. CONCLUSIONS: This study is the first to describe the mutational spectrum of Korean patients with MLC, demonstrating a founder effect of the p.Ala275Asp variant. This study also broadens our understanding of the mutational spectrum of MLC1 by demonstrating a homozygous p.(Ile113Glyfs*4) variant resulting from UPD of chromosome 22.
Alleles ; Chromosomes, Human, Pair 22* ; Comparative Genomic Hybridization ; Exons ; Founder Effect ; Haplotypes ; Humans ; Leukoencephalopathies* ; Loss of Heterozygosity ; Megalencephaly ; Mothers ; Seizures ; Uniparental Disomy*

Pancreatic malignancy is the third leading cause of cancer related death in the United States with limited viable screening options. By the end of this decade, cancers are poised to become the leading cause of death with pancreatic cancer projected to be the second leading cause of cancer related mortality. Pancreatic cystic lesions (PCLs) are found in approximately 5%–14% of patients due to the increased utilization of cross-sectional imaging, with approximately 8%–10% of pancreatic cancers originating as PCLs. Current screening guidelines have shown discrepancies between morphologic characteristics of PCLs and identifying advanced pancreatic disease. Molecular analysis has emerged as a novel technology to aid in adequate diagnosis and management decisions of PCLs. Mucinous cysts including intraductal papillary mucinous neoplasms (IPMNs) or mucinous cystic neoplasms have similar oncogenic mutations including KRAS, TP53, SMAD4, PIK3CA, PTEN, or CKDN2A, while GNAS and RNF43 mutations are specific only to IPMNs. Serous cystadenomas have been associated with a loss of tumor suppressor gene VHL, while solid-psuedopapillary neoplasms have an oncogenic mutation CTNNB1. A specific molecular marker to diagnose existing high-grade dysplasia or impending malignant transformation is yet to be identified. Moving forward it is important to advance technology in isolating and identifying high-risk molecular markers from cyst fluid while considering their increased utilization in the evaluation of PCLs.
Biomarkers, Tumor ; Cause of Death ; Cyst Fluid ; Cystadenoma, Serous ; Diagnosis ; Genes, Tumor Suppressor ; Humans ; Loss of Heterozygosity ; Mass Screening ; Mortality ; Mucins ; Neoplasms, Cystic, Mucinous, and Serous ; Pancreatic Cyst* ; Pancreatic Diseases ; Pancreatic Neoplasms ; United States

PURPOSE: MicroRNAs (miRNAs) are a major class of small endogenous RNA molecules that posttranscriptionally regulate the expression of most genes in the human genome. miRNAs are often located in chromosomal fragile sites, which are suscept-ible to amplification or deletion. Chromosomal deletions are frequent events in breast cancer cells. Deletion and loss of heterozygosity at 17p13.3 have been reported in 49% of breast cancers. The aim of the current study was to evaluate potential expression alterations of miR-22, miR-132, and miR-212, which are located on the 17p13.3 locus and are required for mammary gland development. METHODS: A matched case-control study was conducted, which included 36 pairs of tumor and matched nontumor surgical specimens from patients diagnosed with breast invasive ductal carcinoma. Formalin-fixed paraffin-embedded samples from archival collections at the pathology department of Shariati Hospital were prepared for RNA extraction using the xylene-ethanol method before total RNA was isolated with TRIzol Reagent. Specific primers were designed for cDNA synthesis and miRNA amplification. The expression of miRNAs was then evaluated by real-time polymerase chain reaction (RT-PCR). RESULTS: According to our RT-PCR data, the miR-212/miR-132 family was downregulated in breast cancer (0.328-fold, p<0.001), and this reduced expression was the most prominent in high-grade tumors. In contrast, miR-22 exhibited a significant upregulation in breast tumor samples (2.183-fold, p=0.040). CONCLUSION: Consistent with the frequent deletion of the 17p13.3 locus in breast tumor cells, our gene expression data demonstrated a significant downregulation of miR-212 and miR-132 in breast cancer tissues. In contrast, we observed a significant upregulation of miR-22 in breast tumor samples. The latter conflicting result may have been due to the upregulation of miR-22 in stromal/cancer-associated fibroblasts, rather than in the tumor cells.
Biomarkers ; Breast Neoplasms* ; Breast* ; Carcinoma, Ductal ; Case-Control Studies ; Chromosome Deletion ; DNA, Complementary ; Down-Regulation ; Fibroblasts ; Gene Expression ; Genome, Human ; Humans ; Loss of Heterozygosity ; Mammary Glands, Human ; Methods ; MicroRNAs* ; Pathology ; Real-Time Polymerase Chain Reaction ; RNA ; Up-Regulation