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Deciphering Elevated Microsatellite Alterations at Selected Tetra/Pentanucleotide Repeats, Microsatellite Instability, and Loss of Heterozygosity in Colorectal Cancers.
Wang Y, Vnencak-Jones CL, Cates JM, Shi C
(2018) J Mol Diagn 20: 366-372
MeSH Terms: Adult, Aged, Aged, 80 and over, Colorectal Neoplasms, Female, Humans, Loss of Heterozygosity, Male, Microsatellite Instability, Microsatellite Repeats, Middle Aged
Show Abstract · Added November 1, 2018
Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) are common in colorectal cancers (CRCs). The association between EMAST and classic mono/dinucleotide microsatellite instability (MSI) is unknown. We assessed the stability of 13 tetranucleotide and three pentanucleotide repeat markers in tumor and normal tissue from 22 MSI-high and 107 microsatellite-stable CRC samples. When present, instability was observed at tetra/pentanucleotide repeats and was defined as elevated microsatellite alterations at selected tetra/pentanucleotide repeats-high (EMASTP-H; ≥30% instability), -low (EMASTP-L; <30% instability), or -stable (EMASTP-S). EMASTP instability, including high and low, was observed in 50 of 123 CRCs (41%), including all MSI-high tumors and 28 of 101 microsatellite-stable tumors (28%). MSI-high CRCs were more likely to be EMASTP-H compared with microsatellite-stable tumors with EMASTP instability. Tetranucleotide markers VWA and D13S317 were the two most frequently altered loci. Loss of heterozygosity was more common in EMASTP-L/S than in EMASTP-H CRCs. Frequencies of loss of heterozygosity at three loci were different between EMASTP-L and EMASTP-S tumors. In addition, right-sided tumor site, large tumor size, high tumor grade, and the presence of Crohn-like reaction were significantly associated with EMASTP-H CRCs. However, there were no differences in clinicopathologic features between EMASTP-L and EMASTP-S tumors. In summary, more CRCs exhibited genomic instability as EMASTP than as MSI. EMASTP instability may prove to be an important prognostic/therapeutic indicator in CRCs.
Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
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11 MeSH Terms
Empirical characteristics of family-based linkage to a complex trait: the ADIPOQ region and adiponectin levels.
Hellwege JN, Palmer ND, Mark Brown W, Brown MW, Ziegler JT, Sandy An S, An SS, Guo X, Ida Chen YD, Chen IY, Taylor K, Hawkins GA, Ng MC, Speliotes EK, Lorenzo C, Norris JM, Rotter JI, Wagenknecht LE, Langefeld CD, Bowden DW
(2015) Hum Genet 134: 203-13
MeSH Terms: Adiponectin, Adolescent, Adult, Aged, Aged, 80 and over, Databases, Nucleic Acid, Datasets as Topic, Family, Female, Genetic Linkage, Genetic Loci, Hispanic Americans, Humans, Lod Score, Male, Microsatellite Repeats, Middle Aged, Polymorphism, Single Nucleotide
Show Abstract · Added September 15, 2015
We previously identified a low-frequency (1.1 %) coding variant (G45R; rs200573126) in the adiponectin gene (ADIPOQ) which was the basis for a multipoint microsatellite linkage signal (LOD = 8.2) for plasma adiponectin levels in Hispanic families. We have empirically evaluated the ability of data from targeted common variants, exome chip genotyping, and genome-wide association study data to detect linkage and association to adiponectin protein levels at this locus. Simple two-point linkage and association analyses were performed in 88 Hispanic families (1,150 individuals) using 10,958 SNPs on chromosome 3. Approaches were compared for their ability to map the functional variant, G45R, which was strongly linked (two-point LOD = 20.98) and powerfully associated (p value = 8.1 × 10(-50)). Over 450 SNPs within a broad 61 Mb interval around rs200573126 showed nominal evidence of linkage (LOD > 3) but only four other SNPs in this region were associated with p values < 1.0 × 10(-4). When G45R was accounted for, the maximum LOD score across the interval dropped to 4.39 and the best p value was 1.1 × 10(-5). Linked and/or associated variants ranged in frequency (0.0018-0.50) and type (coding, non-coding) and had little detectable linkage disequilibrium with rs200573126 (r (2) < 0.20). In addition, the two-point linkage approach empirically outperformed multipoint microsatellite and multipoint SNP analysis. In the absence of data for rs200573126, family-based linkage analysis using a moderately dense SNP dataset, including both common and low-frequency variants, resulted in stronger evidence for an adiponectin locus than association data alone. Thus, linkage analysis can be a useful tool to facilitate identification of high-impact genetic variants.
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18 MeSH Terms
Translational research on Barrett's esophagus.
Baruah A, Buttar N, Chandra R, Chen X, Clemons NJ, Compare D, El-Rifai W, Gu J, Houchen CW, Koh SY, Li W, Nardone G, Phillips WA, Sharma A, Singh I, Upton MP, Vega KJ, Wu X
(2014) Ann N Y Acad Sci 1325: 170-86
MeSH Terms: Animals, Barrett Esophagus, Biomarkers, Tumor, Disease Progression, Humans, Microsatellite Repeats, Oxidative Stress, Paris, Translational Medical Research
Show Abstract · Added February 19, 2015
The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentaries on translational research on Barrett's esophagus that address evidence for genetic instability in esophageal cancer; the role of microsatellite instability; the use of histologic and serum Doublecortin-like kinase 1 expression for progression of Barrett's esophagus to adenocarcinoma; the oxidative stress in Barrett's tumorigenesis; the genomic alterations in esophageal cancer; in vivo modeling in Barrett's esophagus; epigenetic and transcriptional regulation in Barrett's esophagus and esophageal adenocarcinoma; and normal and disordered regeneration in Barrett's esophagus.
© 2014 New York Academy of Sciences.
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9 MeSH Terms
Proteogenomic characterization of human colon and rectal cancer.
Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, NCI CPTAC
(2014) Nature 513: 382-7
MeSH Terms: Chromosomes, Human, Pair 20, Colonic Neoplasms, CpG Islands, DNA Copy Number Variations, DNA Methylation, Genomics, Hepatocyte Nuclear Factor 4, Humans, Microsatellite Repeats, Mitochondrial Membrane Transport Proteins, Mutation, Missense, Neoplasm Proteins, Point Mutation, Proteome, Proteomics, Proto-Oncogene Proteins pp60(c-src), RNA, Messenger, RNA, Neoplasm, Rectal Neoplasms, Transcriptome
Show Abstract · Added December 4, 2014
Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon and rectal tumours characterized previously by The Cancer Genome Atlas (TCGA) and perform integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. Messenger RNA transcript abundance did not reliably predict protein abundance differences between tumours. Proteomics identified five proteomic subtypes in the TCGA cohort, two of which overlapped with the TCGA 'microsatellite instability/CpG island methylation phenotype' transcriptomic subtype, but had distinct mutation, methylation and protein expression patterns associated with different clinical outcomes. Although copy number alterations showed strong cis- and trans-effects on mRNA abundance, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. The chromosome 20q amplicon was associated with the largest global changes at both mRNA and protein levels; proteomics data highlighted potential 20q candidates, including HNF4A (hepatocyte nuclear factor 4, alpha), TOMM34 (translocase of outer mitochondrial membrane 34) and SRC (SRC proto-oncogene, non-receptor tyrosine kinase). Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology.
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20 MeSH Terms
A pilot study of microsatellite instability and endometrial cancer survival in white and African American women.
Cote ML, Kam A, Chang CY, Raskin L, Reding KW, Cho KR, Gruber SB, Ali-Fehmi R
(2012) Int J Gynecol Pathol 31: 66-72
MeSH Terms: African Americans, Aged, Aged, 80 and over, Analysis of Variance, DNA, Neoplasm, Endometrial Neoplasms, European Continental Ancestry Group, Female, Genetic Markers, Humans, Hysterectomy, Logistic Models, Michigan, Microsatellite Instability, Microsatellite Repeats, Middle Aged, Neoplasm Staging, Pilot Projects, Prognosis, Retrospective Studies, Survival Analysis
Show Abstract · Added March 5, 2014
Endometrial cancer is the most commonly diagnosed gynecologic malignancy in the United States and can be classified on the basis of various pathologic, molecular, and genetic features, including microsatellite instability (MSI). As MSI is generally associated with a more favorable outcome in colorectal cancers, it is feasible that microsatellite instability may also influence endometrial cancer survival. We examined MSI and survival in 45 African American and 31 white women diagnosed with endometrial cancer at a large, urban cancer center. Fifty-five tumors were classified as type I and 21 tumors were classified as type II. Unconditional logistic regression models found that microsatellite stable tumors were more frequently observed in white women compared with African American women (odds ratio, 8.61; 95% confidence interval, 1.01-73.69). Type I tumors with MSI were not found to be significantly associated with smoking status, tumor stage, or age. Only one type II tumor was classified as MSI. Neither race nor MSI status was a predictor of death from all causes or only endometrial cancer-related deaths were considered in univariate and multivariate survival models. The potential significance of a larger proportion of MSI tumors found in African American women with type I endometrial cancer should be assessed in a larger prospective study.
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21 MeSH Terms
Analysis of microsatellite mutations in buccal cells from a case-control study for lung cancer.
Baumann JL, Li M, Poulsen A, Chadwick NS, Cai Q, Chung CH, Shyr Y, Olsen JH, Zheng W, Slebos RJ
(2012) Cancer Epidemiol 36: e33-9
MeSH Terms: Aged, Case-Control Studies, Female, Humans, Lung Neoplasms, Male, Microsatellite Repeats, Middle Aged, Mouth Mucosa, Mutation, Smoking
Show Abstract · Added March 7, 2014
Exposure to tobacco carcinogens is the major cause of human lung cancer, but even heavy smokers have only about a 10% life-time risk of developing lung cancer. Currently used screening processes, based largely on age and exposure status, have proven to be of limited clinical utility in predicting cancer risk. More precise methods of assessing an individual's risk of developing lung cancer are needed. Because of their sensitivity to DNA damage, microsatellites are potentially useful for the assessment of somatic mutational load in normal cells. We assessed mutational load using hypermutable microsatellites in buccal cells obtained from lung carcinoma cases and controls to test if such a measure could be used to estimate lung cancer risk. There was no significant association between smoking status and mutation frequency with any of the markers tested. No significant association between case status and mutation frequency was observed. Age was significantly related to mutation frequency in the microsatellite marker D7S1482. These observations indicate that somatic mutational load, as measured using mutation frequency of microsatellites in buccal cells, increases with increasing age but that subjects who develop lung cancer have a similar mutational load as those who remain cancer free. This finding suggests that mutation frequency of microsatellite mutations in buccal cells may not be a promising biomarker for lung cancer risk.
Copyright © 2011 Elsevier Ltd. All rights reserved.
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4 Members
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11 MeSH Terms
Information for genetic management of mtDNA disease: sampling pathogenic mtDNA mutants in the human germline and in placenta.
Marchington D, Malik S, Banerjee A, Turner K, Samuels D, Macaulay V, Oakeshott P, Fratter C, Kennedy S, Poulton J
(2010) J Med Genet 47: 257-61
MeSH Terms: Adult, Child, Preschool, DNA, Mitochondrial, Female, Genetic Counseling, Germ-Line Mutation, Humans, Infant, Leigh Disease, Microsatellite Repeats, Mitochondrial Diseases, Oocytes, Placenta, Polymerase Chain Reaction, Pregnancy
Show Abstract · Added May 27, 2014
BACKGROUND - Families with a child who died of severe, maternally inherited mitochondrial DNA (mtDNA) disease need information on recurrence risk. Estimating this risk is difficult because of (a) heteroplasmy-the coexistence of mutant and normal mtDNA in the same person-and (b) the so-called mitochondrial bottleneck, whereby the small number of mtDNAs that become the founders for the offspring cause variation in dose of mutant mtDNA. The timing of the bottleneck and of segregation of mtDNA during foetal life determines the management options. Therefore, mtDNA heteroplasmy was studied in oocytes and placenta of women in affected families.
RESULTS - One mother of a child dying from Leigh syndrome due to the 9176T-->C mtDNA mutation transmitted various loads of mutant mtDNA to < or =3 of 20 oocytes. This was used to estimate recurrence as < or =5%. She subsequently conceived a healthy son naturally. Analysis of the placenta showed that some segregation also occurred during placental development, with the mutant mtDNA load varying by >10% in a placenta carrying 65% 3243A-->G mutant mtDNA.
DISCUSSION - This is the first report of (a) an oocyte analysis for preconception counselling, specifically, refining recurrence risks of rare mutations and (b) a widely different load of a pathogenic mtDNA mutation in multiple oocytes, apparently confined to the germline, in an asymptomatic carrier of an mtDNA disease. This suggests that a major component of the bottleneck occurs during oogenesis, probably early in the foetal life of the mother. The variable mutant load in placenta implies that estimates based on a single sample in prenatal diagnosis of mtDNA disorders have limited accuracy.
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15 MeSH Terms
Homozygosity of the polymorphism MICA5.1 identifies extreme risk of progression to overt adrenal insufficiency among 21-hydroxylase antibody-positive patients with type 1 diabetes.
Triolo TM, Baschal EE, Armstrong TK, Toews CS, Fain PR, Rewers MJ, Yu L, Miao D, Eisenbarth GS, Gottlieb PA, Barker JM
(2009) J Clin Endocrinol Metab 94: 4517-23
MeSH Terms: Addison Disease, Alleles, Autoantibodies, Cross-Sectional Studies, Diabetes Mellitus, Type 1, Disease Progression, Genotype, Graves Disease, HLA-DQ Antigens, HLA-DQ beta-Chains, HLA-DR Antigens, HLA-DRB1 Chains, Histocompatibility Antigens Class I, Homozygote, Humans, Interferon-alpha, Microsatellite Repeats, Polymerase Chain Reaction, Polymorphism, Genetic, Risk Factors, Steroid 21-Hydroxylase
Show Abstract · Added March 29, 2019
CONTEXT - Autoimmunity associated with Addison's disease (AD) can be detected by measuring 21-hydroxylase (21OH) autoantibodies. Subjects with type 1 diabetes (T1D) are at increased risk for AD. Genetic factors including HLA-DRB1*0404 and MICA have been associated with AD in populations with and without T1D.
OBJECTIVE - The objective of the study was to examine the effect of the MICA5.1 allele in subjects with 21OH autoantibodies on progression to AD.
DESIGN - Two components were used: 1) a cross-sectional study with subjects with AD identified and enrolled from September 1993 to November 2008 and 2) a cohort study prospectively following up patients with T1D who screened positive for 21OH autoantibodies.
SETTING - Subjects were identified from the Barbara Davis Center and through the National Adrenal Diseases Foundation.
PATIENTS - Sixty-three subjects with AD were referred through the National Adrenal Diseases Foundation (AD referrals). Sixty-three subjects with positive 21OH antibodies from the Barbara Davis Center were followed up for progression to AD, and 11 were diagnosed with AD (progressors).
RESULTS - Seventy-three percent of progressors (eight of 11) and 57% of AD referrals (36 of 63) were MICA5.1 homozygous (P = ns). Overall, 59% of patients with AD (44 of 74) were MICA5.1/5.1 compared with 17% of nonprogressors (nine of 52) (P < 0.0001) and 19% of normal DR3/4-DQB1*0302 controls (64 of 336) (P < 0.0001).
CONCLUSIONS - Identifying extreme risk should facilitate monitoring of progression from 21OH antibody positivity to overt AD. The HLA-DR3/0404 genotype defines high-risk subjects for adrenal autoimmunity. MICA5.1/5.1 may define those at highest risk for progression to overt AD, a feature unique to AD and distinct from T1D.
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MeSH Terms
Suggestion for linkage of chromosome 1p35.2 and 3q28 to plasma adiponectin concentrations in the GOLDN Study.
Rasmussen-Torvik LJ, Pankow JS, Peacock JM, Borecki IB, Hixson JE, Tsai MY, Kabagambe EK, Arnett DK
(2009) BMC Med Genet 10: 39
MeSH Terms: Adiponectin, Adolescent, Adult, Aged, Aged, 80 and over, Body Mass Index, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 3, Enzyme-Linked Immunosorbent Assay, European Continental Ancestry Group, Female, Fenofibrate, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Hypolipidemic Agents, Lod Score, Male, Microsatellite Repeats, Middle Aged, Minnesota, Utah, Young Adult
Show Abstract · Added April 23, 2015
BACKGROUND - Adiponectin is inversely associated with obesity, insulin resistance, and atherosclerosis, but little is known about the genetic pathways that regulate the plasma level of this protein. To find novel genes that influence circulating levels of adiponectin, a genome-wide linkage scan was performed on plasma adiponectin concentrations before and after 3 weeks of treatment with fenofibrate (160 mg daily) in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study. We studied Caucasian individuals (n = 1121) from 190 families in Utah and Minnesota. Of these, 859 individuals from 175 families had both baseline and post-fenofibrate treatment measurements for adiponectin. Plasma adiponectin concentrations were measured with an ELISA assay. All participants were typed for microsatellite markers included in the Marshfield Mammalian Genotyping Service marker set 12, which includes 407 markers spaced at approximately 10 cM regions across the genome. Variance components analysis was used to estimate heritability and to perform genome-wide scans. Adiponectin was adjusted for age, sex, and field center. Additional models also included BMI adjustment.
RESULTS - Baseline and post-fenofibrate adiponectin measurements were highly correlated (r = 0.95). Suggestive (LOD > 2) peaks were found on chromosomes 1p35.2 and 3q28 (near the location of the adiponectin gene).
CONCLUSION - Two candidate genes, IL22RA1 and IL28RA, lie under the chromosome 1 peak; further analyses are needed to identify the specific genetic variants in this region that influence circulating adiponectin concentrations.
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23 MeSH Terms
Fine mapping and association studies in a candidate region for autism on chromosome 2q31-q32.
Conroy J, Cochrane L, Anney RJ, Sutcliffe JS, Carthy P, Dunlop A, Mullarkey M, O'hici B, Green AJ, Ennis S, Gill M, Gallagher L
(2009) Am J Med Genet B Neuropsychiatr Genet 150B: 535-44
MeSH Terms: Alleles, Autistic Disorder, Chromosome Mapping, Chromosomes, Human, Pair 2, Female, Genetic Predisposition to Disease, Haplotypes, Humans, Integrin alpha4, Karyotyping, Male, Microsatellite Repeats, Mutation, Pedigree, Polymorphism, Single Nucleotide
Show Abstract · Added February 20, 2014
Autism (OMIM %209850) is a neurodevelopmental disorder with a strong genetic component. We previously reported a de novo rearrangement of chromosome 2q31 in a patient with autism [Gallagher et al. (2003); J Autism Dev Disord 33(1):105-108]. Further cytogenetic analysis revealed this to be a 46,XY, t(9;2)(q31.1;q32.2q31.3) translocation. Association mapping with microsatellite and SNP markers of this translocated region on 2q revealed association with markers in Integrin alpha-4 (ITGA4; GeneID 3676). ITGA4 was tested for association in a sample of 179 trio-based families. SNP markers in exons 16 and 17 showed evidence of association. Mutation screening revealed a G to A synonymous variation in the last nucleotide of exon 16 (rs12690517), significantly associated with autism in the Irish sample (OR = 1.6; P = 0.04). The location of this SNP at a putative splice donor site may affect the splicing of the ITGA4 protein. Haplotype analysis showed significant overtransmission of haplotypes surrounding this marker. These markers were investigated in two additional samples, 102 families from Vanderbilt University (VT) (n = 102), and AGRE (n = 267). A non-significant trend towards overtransmission of the associated allele of rs12690517 in the Irish sample (OR = 1.2; P = 0.067) and haplotypes at the 3' end of ITGA4 was observed in the AGRE sample. The VT sample showed association with markers and haplotypes across the gene, but no association with the rs12690517 marker or its surrounding haplotypes. The combined sample showed evidence of association with rs12690517 (OR = 1.3; P = 0.008) and surrounding haplotypes. The findings indicate some evidence for the role of ITGA4 as candidate gene for autism.
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15 MeSH Terms