A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies.

Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, therefore, more useful in genetic correlation with subject phenotype. We describe a new pedigree-based methodology for generating non-ambiguous SNP haplotypes for genetic study. SNP data for haplotype analysis were extracted from a larger Type 1 Diabetes Genetics Consortium SNP dataset based on minor allele frequency variation and redundancy, coverage rate (the frequency of phased haplotypes in which each SNP is defined) and genomic location. Redundant SNPs were eliminated, overall haplotype polymorphism was optimized and the number of undefined haplotypes was minimized. These edited SNP haplotypes from a region containing HLA-DRB1 (DR) and HLA-DQB1 (DQ) both correlated well with HLA-typed DR,DQ haplotypes and differentiated HLA-DR,DQ fragments shared by three pairs of previously identified megabase-length conserved extended haplotypes. In a pedigree-based genetic association assay for type 1 diabetes, edited SNP haplotypes and HLA-typed HLA-DR,DQ haplotypes from the same families generated essentially identical qualitative and quantitative results. Therefore, this edited SNP haplotype method is useful for both genomic polymorphic architecture and genetic association evaluation using SNP markers with diverse minor allele frequencies.

Rectal Suction Biopsy in Patients With Previous Anorectal Surgery for Hirschsprung Disease.

OBJECTIVES: The aim of the study was to determine rates of histologically positive, negative, and inconclusive rectal suction biopsies in post-pull-through patients with Hirschsprung disease evaluated for potential residual aganglionosis at our institution and to determine how patients were managed after a post-pull-through rectal suction biopsy. METHODS: Thirty-nine post-pull-through suction biopsies from our institution were reviewed. Samples, stained with H&E and often acetylcholinesterase and/or calretinin, were categorized as "histologically" positive, negative, or inconclusive for aganglionosis. Subsequent clinical action was categorized as bowel resection, no further procedure, or rebiopsy. Agreement between histologic diagnosis and clinical action was assessed. RESULTS: Histologically, all biopsies were inconclusive (46%) or negative (54%) for residual aganglionosis. Postbiopsy clinical action included redo pull-through (5%), no further procedure (59%), or rebiopsy (36%). Rebiopsy was sought in 2 of 21 histologically negative patients and in only 12 of 18 histologically indeterminate patients. Eventual redo pull-through procedures in 6 of 39 patients showed 4 with residual aganglionosis and 2 with abnormalities suggesting residual "transition zone." CONCLUSIONS: Our findings show that suction biopsy after pull-through was frequently histologically indeterminate and never definitively positive for residual aganglionosis. When biopsy was histologically indeterminate, rebiopsy was pursued less commonly than may be expected. Our findings emphasize that suction biopsy examination is not a "criterion standard" for residual aganglionosis, but instead a component of a diagnosis that ultimately combines clinicopathologic factors, the constellation of which can sometimes spare patients from a more invasive full-thickness biopsy.

Diagnostic Impact of Peritoneal Fluid Cytology in the Setting of Pediatric Uterine Adnexal Biopsy or Resection.

Peritoneal fluid sampling has been recommended during surgery to resect an ovarian or fallopian tube mass, particularly for its staging relevance in ovarian carcinoma. Guidelines specifically for children are not well established, partly because of incomplete knowledge of the test characteristics in this age group. We sought to determine whether peritoneal fluid cytology sampling aids in diagnosis or staging of pediatric uterine adnexal masses. Children who underwent adnexal mass biopsy or excision from 1993 to 2014 were identified via archival review. Accompanying peritoneal fluid (washings or ascites) was assessed to determine whether it provided information beyond that in the accompanying surgical pathology specimen. Of 656 patients who underwent adnexal mass resection, 350 had concurrent cytologic sampling of peritoneal fluid. Median age at surgery was 14 years. Adnexal mass histologic examination showed tumors with malignant potential in 54 (8%) patients. Malignancy was identified in 3 cytology specimens (2 dysgerminomas and 1 mixed germ cell tumor). By today's guidelines, the malignant cytology specimens would have upstaged 1 of the 3 patients, and her therapy may not have changed. Cytology findings did not refine the histologic diagnosis in any benign or malignant case. Our findings demonstrated a low rate of malignancy (<1%) in peritoneal washing/ascites samples accompanying resection of a pediatric adnexal mass. Influencing staging or treatment by cytology sampling was rare in our cohort. Our findings provided benchmark data in an area dominated by adult studies. Furthermore, they may guide recommendations for cytologic fluid collection and processing tailored for pediatric populations.