Molecular Analysis of Gene Amplification in Tumors

Wasson, Jon; Brodeur, Garrett M.

doi:10.1002/0471142905.hg1005s02

Cited by 4 publications

(3 citation statements)

References 31 publications

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“…For the purposes of creating DNA pools, efforts to accurately determine DNA concentrations for each sample are critical because errors will skew the proportion of each genotype in the pool. Spectrophotometric analysis was avoided because substances such as protein and salts may give spurious results (18). The DNA samples were gently mixed on a rocking platform to ensure homogeneity before pipetting.…”

Section: Methodsmentioning

confidence: 99%

Searching for Type 2 Diabetes Genes on Chromosome 20

et al. 2002

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Genome scans in families with type 2 diabetes identified a putative locus on chromosome 20q. For this study, linkage disequilibrium mapping was used in an effort to narrow a 7.3-Mb region in an Ashkenazi type 2 diabetic population. The region encompassed a 1-logarithm of odds (LOD) interval around the microsatellite marker D20S107, which gave a LOD score of >3 in linkage analysis of a combined Caucasian population. This 7.3-Mb region contained 25 known and 99 predicted genes. Predicted single nucleotide polymorphisms (SNPs) were chosen from public databases and validated. Two SNPs were unique to the Ashkenazi. Here, 91 SNPs with a minor allele frequency of >10% were genotyped in pooled DNA from 150 case subjects and 150 control subjects of Ashkenazi Jewish descent. The SNP association study showed that SNP rs2664537 in the TIX1 gene had a significant P value of 0.035, but the finding did not replicate in an additional case pool. In addition, HNF4a and Mybl2 were screened for mutations and new polymorphisms. No mutations were identified, and a new nonsynonymous SNP (R687C in exon 14 of Mybl2) was found. The limits to this type of association study are discussed. Diabetes 51 (Suppl. 3): S308 -S315, 2002 T ype 2 diabetes is a complex metabolic disorder characterized by abnormal hepatic glucose output, insulin resistance, and impaired insulin production (1). Multiple environmental and genetic factors contribute, and genome scans in families with multiple affected individuals from several racial/ethnic groups have been undertaken (Table 1). A number of potential loci have been identified, but in general, the evidence for linkage has not been strong, and the regions identified have been quite broad. A major question remaining is how to proceed with the search for complex disease genes, knowing that a single gene is neither necessary nor sufficient and that recombinant mapping in families will not suffice. The next phase of the search for diabetes susceptibility genes will likely require new strategies.A genome scan with microsatellite markers at an average distance of 9.5 cM was completed in type 2 diabetic sibling pairs (n ϭ 472) of Ashkenazi Jewish descent (2). The Ashkenazi population is relatively young and homogeneous, having undergone several constrictions and expansions resulting in reduced genetic heterogeneity in comparison to that of most Western Caucasian subjects. Studies of DNA polymorphisms have suggested that present-day Ashkenazi Jews descended from a small founder population, numbering perhaps as few as 10,000 individuals who existed in Eastern Europe at about 1500 AD (3). Today, there are about 10 million, representing a 1,000-fold expansion in roughly 20 generations. In the genome scan, five regions on four chromosomes exhibited nominal evidence for linkage (P Ͻ 0.05) (2). A maximal signal of Z ϭ 2.05 was observed on chromosome 20 near D20S195. Because four other groups had previously reported evidence for linkage in the same region of chromosome 20q in Caucasians (see summary in Table 1), this regi...

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Section: Methodsmentioning

confidence: 99%

Searching for Type 2 Diabetes Genes on Chromosome 20

et al. 2002

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“…For the purposes of creating DNA pools, efforts to determine DNA concentrations accurately for each sample are critical, as errors will skew the proportion of each genotype in the pool. Spectrophotometric analysis was avoided because substances such as protein and salts may give spurious results (13). On the other hand, the larger the number of samples in the pool, the less important the individual quantifications become, as random errors in individual samples tend to be minimized in large samples.…”

Section: Dna Isolation and Quantificationmentioning

confidence: 99%

Assessing Allele Frequencies of Single Nucleotide Polymorphisms in DNA Pools by Pyrosequencing ^TM Technology

et al. 2002

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Single nucleotide polymorphism (SNP) association studies searching for differences in allele frequencies between cases and controls have been widely used for genetic analysis. Individual genotyping is prohibitively expensive in large sample sizes. Pooling of samples provides the obvious advantage of higher throughput and lower cost. Here we report our results with the analysis of SNP allele frequencies in DNA pools using Pyrosequencing technology. For seven different SNPs, we observed a mean difference of 1.1 +/- 0.6% between allele frequencies determined in two different DNA pools (n = 150 cases and 150 controls) compared to individually genotyped samples.

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“…At the molecular level, gene amplification may be detected by Southern blot hybridization (see UNIT 10.5;Wasson & Brodeur, 2001), fluorescence in situ hybridization (FISH, see UNIT 4.3;Knoll & Lichter, 2005), chromosomal microarray (UNIT 8.13;Zahir & Marra, 2015), and whole-genome sequencing (Dimmock, 2013;Forozan, Karhu, Kononen, Kallioniemi, & Kallioniemi, 1997;Metzker, 2010;UNIT 9.22). Two of the commonly amplified oncogenes in human cancers include ERBB2 in breast cancer (Eccles, 2001) and MYCN in late-stage neuroblastoma (Kruidering, 2002;Schwab et al, 1983).…”

Section: Activation By Gene Amplificationmentioning

confidence: 99%

Overview of Genetic Diagnosis in Cancer

Korf

Mikhail

2017

CP Human Genetics

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Both cytogenetic and molecular genetic studies can contribute to the management of patients with cancer. In some cases, genetic markers are specific to particular tumor types and are useful in diagnosis. This can be helpful in distinguishing histologically similar tumors that may respond differently to treatment and can sometimes be of prognostic value. Genetic markers can also be tools for following the response of a tumor to therapy, providing a sensitive means to detect relapse. This introductory unit considers some of the types of genetic changes that occur in association with malignancies, as well as major approaches used in their detection. © 2017 by John Wiley & Sons, Inc.

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Molecular Analysis of Gene Amplification in Tumors

Cited by 4 publications

References 31 publications

Searching for Type 2 Diabetes Genes on Chromosome 20

Searching for Type 2 Diabetes Genes on Chromosome 20

Assessing Allele Frequencies of Single Nucleotide Polymorphisms in DNA Pools by Pyrosequencing ^TM Technology

Overview of Genetic Diagnosis in Cancer

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Molecular Analysis of Gene Amplification in Tumors

Cited by 4 publications

References 31 publications

Searching for Type 2 Diabetes Genes on Chromosome 20

Searching for Type 2 Diabetes Genes on Chromosome 20

Assessing Allele Frequencies of Single Nucleotide Polymorphisms in DNA Pools by Pyrosequencing TM Technology

Overview of Genetic Diagnosis in Cancer

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Product

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Assessing Allele Frequencies of Single Nucleotide Polymorphisms in DNA Pools by Pyrosequencing ^TM Technology