The importance of structural variants(SVs)for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical research.To facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-Barr virus(EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV calls.We established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers,including 109x Pacific Biosciences(PacBio)continuous long reads(CLRs),22 x PacBio circular consensus sequencing(CCS)reads,104x Oxford Nanopore Technologies(ONT)long reads,and 114×Bionano optical mapping plat-form,and one de novo assembly-based SV caller using CCS reads.A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing,demonstrating the robustness of our SV calls.Combining trio-binning-based haplotype assemblies,we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions(CHCRs),which covered 1.46 gigabase pairs(Gb)and 6882 SVs supported by at least one diploid haplotype assembly.Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology,disease,and clinical research.

Objective:To establish the industry standard for growth hormone quantitative labelling immunoassay kit, and to validate it by chemiluminescence labeling and time-resolved fluorescence labeling method which are suitable for the standard.Methods: Different assay method kits, including magnetic particle chemiluminescent assay, electrochemiluminescence assay, chemiluminescence assay and time-resolved fluorescent assay, were used to verified the blank limitation, linearity, accuracy, precision, specificity and stability in accordance with protocol industry standard.Results: Other verification results could meet requirements of the protocol industry standard besides accuracy in part of kits couldn't achieve to anticipative remand (relative deviation couldn't be more than ±10%).Conclusion: According to the verification results, the accuracy requirements was adjusted to ±15%. The other items of industry standard were maintained. The industry standard for growth hormone quantitative labeling immunoassay kit is ultimately established. The standard would contribute to unity quality standard of growth hormone quantitative labeling immunoassay kit, and provide the basis for the supervision and administration of its production, examination, circulation, clinical application and other areas.

OBJECTIVETo study the reasons for the discrepancies in pathologic diagnosis of gastric dysplasia/early cancer in endoscopic submucosal dissection (ESD) specimens, and how to cope with the discrepancies.

METHODSThe pathologic diagnoses in 60 cases of ESD specimens according to the three currently used classification systems (namely Western criteria, Japanese criteria and Vienna classification) were compared. The diagnostic discrepancies were analyzed.

RESULTSFifteen of the 17 cases diagnosed as low-grade intraepithelial neoplasia according to the Western criteria were revised as adenoma by the Japanese criteria. Amongst the 43 cases of gastric intramucosal adenocarcinoma diagnosed according to the Japanese criteria, 23 cases had concordant diagnosis by the Western criteria. While the diagnosis of low-grade intraepithelial neoplasia/adenoma was basically similar irrespective of classification system used, there were significant differences in the interpretation of gastric early cancer.

CONCLUSIONSThe diagnostic discrepancies in the gastric dysplasia/early cancer are mainly related to the morphologic criteria applied in different classifications. In order to facilitate clinical and pathologic communication, a consensus using Vienna/WHO classifications, supplemented with Japanese system, is desirable.

Adenoma ; pathology ; Carcinoma in Situ ; pathology ; Dissection ; methods ; Gastroscopy ; Humans ; Hyperplasia ; pathology ; Stomach ; pathology ; Stomach Neoplasms ; pathology

OBJECTIVETo evaluate the quality status of rubella virus IgM diagnostic kits by national supervising sampling.

METHODSUsing legal inspection combining with exploratory study, the positive and negative coincidence rate, detection limit and repeatability of kits were verified.

RESULTSThe results showed that 15 of 16 batches of kits were qualified using legal inspection, and the passing rate was 93.8%. The unqualified item was negative coincidence rate. In exploratory study, only 11 batches (68.8%) complied with industry standard. The unqualified items were negative coincidence rate, detection limit and repeatability.

CONCLUSIONAt present, rubella virus IgM diagnostic Kits have some quality problems in the market. It is recommended that we adopt industry standard and national reference panel in the registration inspection for the future, which will prompt enterprises to improve quality.

Antibodies, Viral ; Humans ; Immunoglobulin M ; Quality Control ; Reagent Kits, Diagnostic ; standards ; Rubella ; diagnosis ; Rubella virus

Objective To evaluate the quality status of rubel a virus IgM diagnostic kits by national supervising sampling. Methods Using legal inspection combining with exploratory study, the positive and negative coincidence rate, detection limit and repeatability of kits were verified. Results The results showed that 15 of 16 batches of kits were qualified using legal inspection, and the passing rate was 93.8%. The unqualified item was negative coincidence rate. In exploratory study, only 11 batches (68.8%) complied with industry standard. The unqualified items were negative coincidence rate, detection limit and repeatability. Conclusion At present, rubel a virus IgM diagnostic Kits have some quality problems in the market. It is recommended that we adopt industry standard and national reference panel in the registration inspection for the future, which wil prompt enterprises to improve quality.

Biopsy ; Dissection ; Gastric Mucosa ; pathology ; surgery ; Gastroscopy ; methods ; Humans ; Neoplasm Invasiveness ; Neoplasm Staging ; Neoplastic Cells, Circulating ; Stomach Neoplasms ; pathology ; surgery ; Stomach Ulcer ; pathology

Autoimmune Diseases ; metabolism ; pathology ; surgery ; Chromogranin A ; metabolism ; Female ; Gastrectomy ; Gastric Mucosa ; pathology ; Gastrin-Secreting Cells ; metabolism ; pathology ; Gastrins ; metabolism ; Gastritis, Atrophic ; metabolism ; pathology ; surgery ; Humans ; Hyperplasia ; Middle Aged ; Mucin-6 ; metabolism ; Neuroendocrine Tumors ; metabolism ; pathology ; surgery ; Stomach ; pathology ; surgery ; Stomach Neoplasms ; metabolism ; pathology ; surgery ; Synaptophysin ; metabolism

Objective To prepare the HPV genotyping control materials. Methods Three hundred cervical smears with different HPV genotypes were collected and detected by surface plasmon resonance and sequencing. The primers for specific genotype were designed according to GenBank. The recombinant plasmid was constructed through PCR amplification, ligation and transformation. Thirty recombinant plasmids were identified through PCR amplification, sequencing, and the sequences were compared using BLAST. Results The collected HPV infectious samples contained 30 different genotypes including HPV 6,16,18 and so on.The fragment sequences of PCR amplification were concordant with the designed. The fragment sizes of the other types ranged from 1 500 to 2 000 bp except HPV CP8304. And the 30 recombinant plasmids identified by PCR were concordant with the target. The identity of BLAST was 99%. In the fragment of 1500 bp in length, 11 bases were inconsistent with the reference sequence. Conclusions Genotyping control materials were developed successfully. The human papillomavirns genotyping control materials covered all the most common types and included 14 types with high-risk, 3 types with medium-risk and 13 types with low-risk.

OBJECTIVETo study the influence of heat-induced epitope retrieval (HIER) on endogenous avidin-binding activity (EABA) and to establish an effective way to block EABA in immunohistochemistry.

METHODSSystematically screening EABA in 164 (679 samples) formalin-fixed and paraffin-embedded human tissues including 76 (102 samples) normal tissues and 88 (577 samples) tumor tissues as well as 4 (80 samples) formalin-fixed and paraffin-embedded rat normal tissues using tissue array (tissue chip), HIER, immunohistochemistry and egg white solution blocking. In addition, EABA was also examined in 9 (15 samples) human frozen tissues.

RESULTS(1) EABA was detected in frozen tissues. (2) No staining for EABA was seen in formalin-fixed and paraffin-embedded tissues. (3) EABA was revealed after the tissues treated with microwave HIER. (4) The density of signal for EABA was variable from tissue to tissue and cell to cell. (5) The signals of EABA expressed in scatter or diffuse in tissues and in granular form in cytoplasm. (6) EABA was found in a wide range of epithelial tissues, especially in gland epithelia of normal and tumor tissues. These included kidney, adrenal cortex, liver, C cells of thyroid gland, oxyphil cells of parathyroid, fundal gland of stomach, sebaceous gland of skin, duct of salivary; oncocytoma and papillary adenocarcinoma of kidney and thyroid gland, adenolymphoma of parotid, carcinoma of liver cell, adenocarcinoma of stomach, colon, prostate, gall bladder and endometrium, and so on. (7) EABA was easier revealed by higher pH value buffer (EGTA pH 9.0) than that with lower pH value (EDTA pH 8.0 and citrate pH 6.0). (8) The revealed EABA could be effectively blocked using 20% egg white solution.

CONCLUSIONSHIER could unmask EABA in formalin-fixed and paraffin-embedded tissues. The unmasked EABA present in a wide range of human normal and tumor tissues as well as in rat normal tissues. The EABA could influence routine immunohistochemistry staining when using (strept)avidin-horseradish peroxidase detective system. The egg white solution could effectively block EABA and eliminate the influence of EABA on immunohistochemistry.

Animals ; Avidin ; antagonists & inhibitors ; metabolism ; Biotin ; metabolism ; Cells, Cultured ; Egg Proteins ; pharmacology ; Epithelial Cells ; metabolism ; Epitopes ; Female ; Hot Temperature ; Humans ; Immunohistochemistry ; Male ; Neoplasms ; metabolism ; pathology ; Rats

OBJECTIVETo investigate the morphologic features and diagnostic criteria of various types pf renal adenomas of the kidney.

METHODSIn addition to light microscopy, electron microscopy, histochemical and immunohistochemical assays were applied. All 19 cases of adenomas were followed up.

RESULTSThree (3) cases of papillary adenoma were featured as papillary or tubulopapillary growth in patterns consisting of tumor cells with basophilic or acidophilic cytoplasm and were positive for both epithelial membrane antigen (EMA) and cytokeratin (CK7). Thirteen (13) cases of oncocytoma were characterized by the diversity of the structures including to be nest, tubular and papillary in pattern; a mixture of cell types including the classic oncocytes, oncoblasts and clear cells which were negative for vimentin and CK7 but positive for EMA. Enormous large mitochondria were obtained in 4 cases of oncocytoma by electronic microscopy. Three (3) cases of metanephric adenoma consisted of closely packed, round tubules lined by small bland cells with solid, glomeruloid constructure. Branching, elongated tubules and polypoid fronds were also detected. Tumor cells were negative for EMA, negative or only focally positive for CK7. Eighteen (18) patients were alive except one oncocytoma patient died 5 years after the diagnosis convinced. All the cases reported in this article had been followed up of 3 - 5 years.

CONCLUSIONSThere are 3 kinds of renal adenomas, namely, the papillary adenoma, oncocytoma, and metanephric adenoma and each kind has its own clincopathological features. The latter two can be recognized by their distinctive morphology, and the former can only be diagnosed according to the size of the tumor as the reference. Histochemical and immohistochemical assays are helpful in differential diagnosis.

Adenoma ; Adenoma, Oxyphilic ; Diagnosis, Differential ; Humans ; Kidney ; Kidney Neoplasms