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Number Determination (number + determination)
Selected AbstractsHigh-resolution mapping of the 8p23.1 beta-defensin cluster reveals strictly concordant copy number variation of all genes,HUMAN MUTATION, Issue 10 2008Marco Groth Abstract One unexpected feature of the human genome is the high structural variability across individuals. Frequently, large regions of the genome show structural polymorphisms and many vary in their abundance. However, accurate methods for the characterization and typing of such copy number variations (CNV) are needed. The defensin cluster at the human region 8p23.1 is one of the best studied CNV regions due to its potential clinical relevance for innate immunity, inflammation, and cancer. The region can be divided into two subclusters, which harbor predominantly either alpha- or beta-defensin genes. Previous studies assessing individual copy numbers gave different results regarding whether the complete beta-defensin cluster varies or only particular genes therein. We applied multiplex ligation-dependent probe amplification (MLPA) to measure defensin locus copy numbers in 42 samples. The data show strict copy number concordance of all 10 loci typed within the beta-defensin cluster in each individual, while seven loci within the alpha-defensin cluster are consistently found as single copies per chromosome. The exception is DEFA3, which is located within the alpha-defensin cluster and was found to also differ in copy number interindividually. Absolute copy numbers ranged from two to nine for the beta-defensin cluster and zero to four for DEFA3. The CNV-typed individuals, including HapMap samples, are publicly available and may serve as a universal reference for absolute copy number determination. On this basis, MLPA represents a reliable technique for medium- to high-throughput typing of 8p23.1 defensin CNV in association studies for diverse clinical phenotypes. Hum Mutat 0,1,8, 2008. © 2008 Wiley-Liss, Inc. [source] Determination of genomic copy number with quantitative microsphere hybridization,,HUMAN MUTATION, Issue 4 2006Heather L. Newkirk Abstract We developed a novel quantitative microsphere suspension hybridization (QMH) assay for determination of genomic copy number by flow cytometry. Single copy (sc) products ranging in length from 62 to 2,304 nucleotides [Rogan et al., 2001; Knoll and Rogan, 2004] from ABL1 (chromosome 9q34), TEKT3 (17p12), PMP22 (17p12), and HOXB1 (17q21) were conjugated to spectrally distinct polystyrene microspheres. These conjugated probes were used in multiplex hybridization to detect homologous target sequences in biotinylated genomic DNA extracted from fixed cell pellets obtained for cytogenetic studies. Hybridized targets were bound to phycoerythrin-labeled streptavidin; then the spectral emissions of both target and conjugated microsphere were codetected by flow cytometry. Prior amplification of locus-specific target DNA was not required because sc probes provide adequate specificity and sensitivity for accurate copy number determination. Copy number differences were distinguishable by comparing the mean fluorescence intensities (MFI) of test probes with a biallelic reference probe in genomic DNA of patient samples and abnormal cell lines. Concerted 5, ABL1 deletions in patient samples with a chromosome 9;22 translocation and chronic myelogenous leukemia were confirmed by comparison of the mean fluorescence intensities of ABL1 test probes with a HOXB1 reference probe. The relative intensities of the ABL1 probes were reduced to 0.59±0.02 &!ndash;fold in three different deletion patients and increased 1.42±0.01 &!ndash;fold in three trisomic 9 cell lines. TEKT3 and PMP22 probes detected proportionate copy number increases in five patients with Charcot-Marie-Tooth Type 1a disease and chromosome 17p12 duplications. Thus, the assay is capable of distinguishing one allele and three alleles from a biallelic reference sequence, regardless of chromosomal context. Hum Mutat 27(4), 376,386, 2006. © 2006 Wiley-Liss, Inc. [source] A test of three hypotheses for ovariole number determination in the grasshopper Romalea micropteraPHYSIOLOGICAL ENTOMOLOGY, Issue 3 2010BENJAMIN J. TAYLOR Ovariole number in insects determines potential fecundity and can be influenced by genes, environmental conditions during development and parental effects. In the present study, three hypotheses are tested for ovariole number determination in the grasshopper Romalea microptera (Beauvois), which exhibits both intra- and interpopulation variation in ovariole number. In hypothesis 1, variation in ovariole number is a result of genetic variation. In hypothesis 2, ovariole number is influenced by nutrition during development. In hypothesis 3, ovariole number is influenced by maternal nutritional status. Females from four treatments are compared: low-food, high-food, daughters of low-food, and daughters of high-food. There is a relationship between parent and offspring ovariole number despite different environments, supporting hypothesis 1. Also, ovariole numbers are slightly, but significantly lower in individuals fed a low-food diet compared with a high-food diet, supporting hypothesis 2. Hypothesis 3 is not supported: starved and well-fed females produce eggs of similar mass, as well as offspring with similar numbers of ovarioles, suggesting that the nutritional status of mothers does not influence offspring mass or offspring ovariole number. The results imply that genetic variation and developmental conditions determine ovariole number in this species but maternal environment does not. These results conflict with previous studies of ovariole determination in grasshoppers and locusts. [source] Real-time PCR-based determination of gene copy numbers in Pichia pastorisBIOTECHNOLOGY JOURNAL, Issue 4 2010Sandra Abad Abstract Pichia pastoris is a preferred host for heterologous protein production. Expression cassettes are usually integrated into the genome of this methylotrophic yeast. This manuscript describes a method for fast and reliable gene copy number determinations for P. pastoris expression strains. We believe that gene copy number determinations are important for all researchers working with P. pastoris and also many other research groups using similar gene integration techniques for the transformation of other yeasts. The described method uses real-time PCR to quantify the integrated expression cassettes. Similar methods were employed previously for other host systems such as animal and plant cells but no such method comparing different detection methods and describing details for yeast analysis by quantitative PCR is known to us, especially for methylotrophic yeasts such as P. pastoris. Neglecting gene copy numbers can easily lead to false interpretations of experimental results from codon optimization or promoter studies and co-expression of helper proteins as demonstrated in an application example, which is also described here. [source] | ||||||||||