This study aims to clarify host factors of IFN treatment in the treatment of chronic hepatitis B (CHB) patients by screening the differentially expressed genes of IFN pathway CHB patients with different response to interferon (IFN) therapy. Three cases were randomly selected in IFN-responding CHB patients (Rs), non-responding CHB patients (NRs) and healthy participants, respectively. The human type I IFN response RT ² profiler PCR array was used to detect the expression levels of IFN-related genes in peripheral blood monocytes (PBMCs) from healthy participants and CHB patients before and after Peg-IFN-α 2a treatment. The results showed that more differentially expressed genes appeared in Rs group than NRs group after IFN treatment. Comparing with healthy participants, IFNG, IL7R, IRF1, and IRF8 were downregulated in both Rs and NRs group before IFN treatment; CXCL10, IFIT1, and IFITM1 were upregulated in the Rs; IL13RA1 and IFI35 were upregulated in the NRs, while IFRD2, IL11RA, IL4R, IRF3, IRF4, PYHIN1, and ADAR were downregulated. The expression of IL15, IFI35 and IFI44 was downregulated by 4.09 ( t = 10.58, P < 0.001), 5.59 ( t = 3.37, P = 0.028) and 10.83 ( t = 2.8, P = 0.049) fold in the Rs group compared with the NRs group, respectively. In conclusion, IFN-response-related gene array is able to evaluate IFN treatment response by detecting IFN-related genes levels in PBMC. High expression of CXCL10, IFIT1 and IFITM1 before treatment may suggest satisfied IFN efficacy, while high expression of IL13RA1, IL15, IFI35 and IFI44 molecules and low expression of IFRD2, IL11RA, IL4R, IRF3, IRF4, PYHIN1 and ADAR molecules may be associated with poor IFN efficacy.
Humans ; Healthy Volunteers ; Hepatitis B, Chronic/genetics* ; Immunotherapy ; Interleukin-15 ; Leukocytes, Mononuclear ; Nuclear Proteins ; Oligonucleotide Array Sequence Analysis/methods* ; Interferons/therapeutic use* ; Treatment Outcome

Canine MDR1 gene mutations produce translated P-glycoprotein, an active drug efflux transporter, resulting in dysfunction or over-expression. The 4-base deletion at exon 4 of MDR1 at nucleotide position 230 (nt230[del4]) in exon 4 makes P-glycoprotein lose function, leading to drug accumulation and toxicity. The G allele of the c.-6-180T>G variation in intron 1 of MDR1 (single nucleotide polymorphism [SNP] 180) causes P-glycoprotein over-expression, making epileptic dogs resistant to phenobarbital treatment. Both of these mutations are reported to be common in collies. This study develops a more efficient method to detect these two mutations simultaneously, and clarifies the genotype association with the side effects of chemotherapy. Genotype distribution in Taiwan was also investigated. An oligonucleotide microarray was successfully developed for the detection of both genotypes and was applied to clinical samples. No 4-base deletion mutant allele was detected in dogs in Taiwan. However, the G allele variation of SNP 180 was spread across all dog breeds, not only in collies. The chemotherapy adverse effect percentages of the SNP 180 T/T, T/G, and G/G genotypes were 16.7%, 6.3%, and 0%, respectively. This study describes an efficient way for MDR1 gene mutation detection, clarifying genotype distribution, and the association with chemotherapy.
Alleles ; Animals ; Dogs ; Drug Therapy ; Exons ; Genotype ; Introns ; Methods ; Oligonucleotide Array Sequence Analysis ; P-Glycoprotein ; Phenobarbital ; Taiwan

OBJECTIVE: To assess the clinical application of single nucleotide polymorphism microarray (SNP array) in prenatal genetic diagnosis for fetuses with absent nasal bone. METHODS: Seventy four fetuses with absent nasal bone detected by prenatal ultrasound scanning were recruited from Women's Hospital, Zhejiang University School of Medicine during June 2015 and October 2018. The chromosome karyotypes analysis and SNP array were performed. The correlation between absent fetal nasal bone and chromosome copy number variants was analyzed. RESULTS: Among 74 fetuses, 19 were detected to have chromosomal abnormalities, including 16 cases of trisomy-21, 1 case of trisomy-18 and two cases of micro-deletion/duplication. Among 46 cases with isolated absence of nasal bone, 3 had trisomy-21, and 1 had a micro-duplication. Absence of nasal bone in association with nuchal translucency thickening had a higher rate of abnormal karyotypes compared with isolated absence of nasal bone (=32.27,<0.01). CONCLUSIONS Fetuses with absent nasal bone and nuchal translucency thickening are likely to have chromosome abnormalities, and SNP array testing is recommended to exclude the chromosome abnormalities.
Chromosome Aberrations ; Female ; Fetus ; Humans ; Nasal Bone ; abnormalities ; Oligonucleotide Array Sequence Analysis ; standards ; Polymorphism, Single Nucleotide ; genetics ; Pregnancy ; Pregnancy Trimester, First ; Prenatal Diagnosis ; methods

OBJECTIVETo explore the clinical and genetic characteristics of a case with Pallister-Killian syndrome (PKS).

METHODSChromosomal karyotype of umbilical cord blood sample derived from a 36-year-old pregnant woman was analyzed by G-banding analysis. After birth, the child was further analyzed with single nucleotide polymorphism microarray (SNP array) and fluorescence in situ hybridization (FISH) using 12pter/12qter probes.

RESULTSG-banding analysis showed that the fetus has a karyotype of 46,XY [77]/47,XY,+mar [23]. After birth, Affymetrix CytoScan 750K array analysis showed a segmental tetrasomy of arr [hg19] 12p13.33p11.1(173 786 - 34 835 641)×4 and a 34.6 Mb repeat at 12p13.33p11.1 with in the neonate. FISH analysis confirmed that 39% of cells harbored the 12p tetrasomy.

CONCLUSIONCombined clinical examination, G-banded chromosomal karyotyping, FISH and microarray analysis can delineate the origin and fragments of small supernumerary marker chromosomes and diagnose PKS with precision.

Adult ; Chromosome Banding ; Chromosome Disorders ; diagnosis ; Chromosomes, Human, Pair 12 ; Female ; Humans ; In Situ Hybridization, Fluorescence ; methods ; Karyotyping ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; Pregnancy ; Prenatal Diagnosis ; methods

BACKGROUND: Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. METHODS: Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). RESULTS: Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. CONCLUSIONS: Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations.
DNA* ; Genotype ; Humans* ; Mass Screening ; Methods* ; Oligonucleotide Array Sequence Analysis* ; Uterine Cervical Neoplasms

BACKGROUND/AIMS: The failure to correctly differentiate between intrahepatic cholangiocarcinoma (CC) and hepatocellular carcinoma (HCC) is a significant clinical problem, particularly in terms of the different treatment goals for both cancers. In this study a specific gene expression profile to discriminate these two subgroups of liver cancer was established and potential diagnostic markers for clinical use were analyzed. METHODS: To evaluate the gene expression profiles of HCC and intrahepatic CC, Oligonucleotide arrays (AffymetrixU133A) were used. Overexpressed genes were checked for their potential use as new markers for discrimination and their expression values were validated by reverse transcription polymerase chain reaction and immunohistochemistry analyses. RESULTS: 695 genes/expressed sequence tags (ESTs) in HCC (245 up-/450 down-regulated) and 552 genes/ESTs in CC (221 up-/331 down-regulated) were significantly dysregulated (p < 0.05, fold change >2, ≥70%). Using a supervised learning method, and one-way analysis of variance a specific 270-gene expression profile that enabled rapid, reproducible differentiation between both tumors and non-malignant liver tissues was established. A panel of 12 genes (e.g., HSP90β, ERG1, GPC3, TKT, ACLY, and NME1 for HCC; SPT2, T4S3, CNX43, TTD1, HBD01 for CC) were detected and partly described for the first time as potential discrimination markers. CONCLUSIONS: A specific gene expression profile for discrimination of primary liver cancer was identified and potential marker genes with feasible clinical impact were described.
Carcinoma, Hepatocellular ; Cholangiocarcinoma ; Discrimination (Psychology)* ; Gene Expression* ; Immunohistochemistry ; Learning ; Liver Neoplasms ; Liver* ; Methods ; Oligonucleotide Array Sequence Analysis* ; Polymerase Chain Reaction ; Reverse Transcription ; Transcriptome

OBJECTIVETo explore the value of single nucleotide polymorphism array (SNP-array) for the analysis of pediatric patients with growth retardation.

METHODSOne hundred eighty one children with growth retardation were enrolled. DNA was extracted from peripheral samples from the patients, and whole genome copy number variations (CNVs) were detected using Illumina Human Cyto SNP-12. All identified CNVs were further analyzed with reference to databases including ClinGen, ClinVar, DECIPHER, OMIM and DGV as well as comprehensive review of literature from PubMed to determine their pathogenicity.

RESULTSForty seven patients (26%) with abnormal CNVs were detected, which included 12 known microdeletions/microduplications syndrome (26%), 10 pathogenic non-syndromic CNVs (21%), 3 numerical chromosome aberrations (6%), 3 unbalanced translocations (6%), 4 pathogenic mosaicisms (9%) and 15 cases with unknown clinical significance (32%). After excluding obvious numerical and/or structural chromosomal abnormalities, this study has detected 15 pathogenic microdeletions/microduplications sized 5 Mb or less, which may be missed by routine chromosomal karyotyping. In addition, there were 3 cases with loss of heterozygoisty (LOH) containing known or predicted imprinting genes as well as 2 cases with suspected parental consanguinity.

CONCLUSIONSNP-array technology is a powerful tool for the genetic diagnosis of children with growth disorders with advantages of high resolution and improved accuracy.

Adolescent ; Child ; Child, Preschool ; Chromosome Aberrations ; DNA Copy Number Variations ; Developmental Disabilities ; diagnosis ; genetics ; Female ; Humans ; Infant ; Karyotyping ; Male ; Oligonucleotide Array Sequence Analysis ; methods ; Polymorphism, Single Nucleotide

OBJECTIVE: The aim of this study was to describe the principle of the Cheil HPV DNA Chip assay and evaluate its accuracy. In order to quantify the human papillomavirus (HPV) load and identify HPV genotypes simultaneously, this assay combined the two methods: SYBR Green quantitative real-time polymerase chain reaction (PCR) and DNA microarray. METHODS: We designed novel consensus primer sets that target the conserved region of the HPV L1 gene for quantifying and detecting a broad range of HPV types by quantitative real-time PCR. Subsequently, using the PCR products, DNA microarray was performed with 36 HPV type-specific probes. To validate this method, direct sequencing and correlation analysis among HPV genotype, viral load, and cytological abnormality was performed by Cohen’s kappa values, two-sided McNemar chi-square test, Kruskal-Wallis test, and odds ratios. RESULTS: The kappa value of the Cheil HPV DNA Chip was 0.963 (95% confidence interval, 0.919 to 0.98), which was significantly higher than the value of 0.527 (95% confidence interval, 0.447 to 0.59) obtained using a conventional HPV DNA Chip. HPV16 (χ²=62.28, P<0.01), HPV33 (χ²=7.18, P<0.01), and HPV58 (χ²=9.52, P<0.01), which are classified as high-risk HPVs, were detected at significant levels in samples with high-grade lesions. And viral loads tended to be higher in groups with high odds ratios. CONCLUSION: The Cheil HPV DNA Chip is an effective diagnostic assay for simultaneously detecting HPV genotypes and loads in cervical samples.
Consensus ; Diagnosis ; Genotype* ; Humans* ; Methods* ; Odds Ratio ; Oligonucleotide Array Sequence Analysis ; Papillomaviridae ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction* ; Viral Load

OBJECTIVETo explore the genetic cause for a boy featuring mainly with mental retardation.

METHODSG-banding karyotyping and fluorescence in situ hybridization (FISH) were carried out for the child and his parents. The child was also analyzed with chromosome microarray (CMA). Suspected microdeletion was validated with quantitative PCR.

RESULTSThe proband was found to have a 47,XYY karyotype by both chromosome and FISH analyses, while both of his parents had a normal karyotype. CMA suggested that the proband had one copy of X chromosome and two copies of Y chromosome. In addition, CMA has also detected deletion of the KYNU gene (mapped at 2q22.2), which could be pathogenic. The result was confirmed by qPCR.

CONCLUSIONFor its high resolution, CMA can be used to identify potential microdeletion/duplications among children with chromosome aneuploidy and unusual phenotypes.

Adult ; Child, Preschool ; Chromosome Banding ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Intellectual Disability ; genetics ; Karyotyping ; Male ; Oligonucleotide Array Sequence Analysis ; methods ; Polymorphism, Single Nucleotide ; Sex Chromosome Disorders ; diagnosis ; genetics ; XYY Karyotype ; diagnosis ; genetics

OBJECTIVETo explore the origin of a supernumerary small marker chromosome (sSMC) in a fetus, and to assess the feasibility of single nucleotide polymorphism array (SNP-array) for prenatal diagnosis.

METHODSThe fetal sample was subjected to karyotyping analysis. The identified sSMC was subjected to genome-wide scan using a SNP microarray chip. The results were validated with fluorescence in situ hybridization (FISH).

RESULTSThe karyotype of the fetus was determined as 47,XX,+mar, which was verified by SNP microarray chip analysis as a 34.6 Mb duplication in 12p13.33p11.1. FISH analysis confirmed that the sSMC has originated from chromosome 12p.

CONCLUSIONThe karyotype of the fetus was determined as 47,XX,+i(12)(p10). Tetrasomy 12p is reported to be a marker for Pallister-Killian syndrome, which may result in multi-system anomalies. SNP-array analysis can simultaneously detect microdeletions and microduplications, which may be used for prenatal diagnosis of suspected cases.

Adult ; Chromosome Aberrations ; Chromosome Banding ; Chromosome Disorders ; diagnostic imaging ; embryology ; genetics ; Chromosomes, Human, Pair 12 ; genetics ; Female ; Fetus ; abnormalities ; diagnostic imaging ; metabolism ; Genome-Wide Association Study ; methods ; Humans ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Oligonucleotide Array Sequence Analysis ; methods ; Polymorphism, Single Nucleotide ; Pregnancy ; Ultrasonography, Prenatal ; methods