Search results for "DUP"

An FPGA aligner for short read mapping

2012

The rapid growth of short read datasets poses a new challenge to the mapping of short reads to a reference genome in terms of sensitivity and execution speed. In this work, we present a parallel architecture for short read mapping utilizing field programmable gate array (FPGA)-based hardware. The computation intensive semi-global alignment and the hash table lookup operations are mapped onto an FPGA. The proposed Align Core is implemented with a parallel block structure to gain computational efficiency. We present a new parallel block-wise alignment structure to approximate the conventional dynamic programming algorithm. The performance of our FPGA aligner is compared to the GASSST and BWA …

Active learning strategies for the deduplication of electronic patient data using classification trees.

2012

Graphical abstractDisplay Omitted Highlights? Active learning for medical record linkage is used on a large data set. ? We compare a simple active learning strategy with a more sophisticated variant. ? The active learning method of Sarawagi and Bhamidipaty (2002) 6] is extended. ? We deliver insights into the variations of the results due to random sampling in the active learning strategies. IntroductionSupervised record linkage methods often require a clerical review to gain informative training data. Active learning means to actively prompt the user to label data with special characteristics in order to minimise the review costs. We conducted an empirical evaluation to investigate whether…

Polycystic ovarian syndrome: assessment with color Doppler angiography and three-dimensional ultrasonography.

1999

We conducted a three-dimensional ultrasonographic evaluation of the size and structure of the ovaries of women who had clinical and biochemical findings suggestive of polycystic ovary syndrome. We carried out a comparative color Doppler frequency and color Doppler amplitude study of the vascular patterns of these ovaries. This study involved 65 women of reproductive age with polycystic ovary syndrome and 25 eumenorrheic women who were not taking hormonal contraceptives and who had a body mass index below 25 kg/m2. Compared to controls, women with polycystic ovary syndrome had larger ovaries and thicker stroma, increased impedance in the uterine arteries, increased stromal vascularity with d…

Genetic alterations and oxidative metabolism in sporadic colorectal tumors from a Spanish community

1997

Deletions of loci on chromosomes 5q, 17p, 18q, and 22q, together with the incidence of p53 mutations and amplification of the double minute-2 gene were investigated in the sporadic colorectal tumors of 44 patients from a Spanish community. Chromosome deletions were analyzed by means of loss of heterozygosity analysis using a restriction fragment length polymorphism assay. Allelic losses were also detected by polymerase chain reaction (PCR)-single-stranded conformation polymorphism (SSCP) analysis of a polymorphic site in intron 2 of the p53 gene. The percentages of genetic deletions on the screened chromosomes were 39.3% (5q), 58.3% (17p), 40.9% (18q), and 40% (22q). Mutations in p53 exons …

A prenatal case of inverted duplication with terminal deletion of 5p not including the cat-like cry critical region

2010

Mutation spectrum and clinical investigation of achromatopsia patients with mutations in the GNAT2 gene

2019

Achromatopsia (ACHM) is a hereditary cone photoreceptor disorder characterized by the inability to discriminate colors, nystagmus, photophobia, and low-visual acuity. Six genes have been associated with this rare autosomal recessively inherited disease, including the GNAT2 gene encoding the catalytic α-subunit of the G-protein transducin which is expressed in the cone photoreceptor outer segment. Out of a cohort of 1,116 independent families diagnosed with a primary clinical diagnosis of ACHM, we identified 23 patients with ACHM from 19 independent families with likely causative mutations in GNAT2, representing 1.7% of our large ACHM cohort. In total 22 different potentially disease-causing…

Single-Nucleotide Polymorphism Array-Based Karyotyping of Acute Promyelocytic Leukemia

2014

Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), but additional chromosomal abnormalities (ACA) and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A) 6.0 (Affymetrix) in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%): 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH), being a duplication of 8(q24) (23%) and a deletion of 7(q33-qter) (…

Rapid and reliable genotyping procedure for detection of alleles with mutations, deletion, or/and duplication of the CYP2D6 gene

2009

Abstract Background Polymorphisms of cytochrome P450 2D6 (CYP2D6) have a significant effect on the pharmacokinetics of most tricyclic antidepressants. More than 150 alleles lead to four distinct phenotypes of drug metabolism. The phenotypes are described as ultrarapid, extensive, intermediate, and poor metabolizers. Therapeutic plasma levels of CYP2D6 substrates may be difficult to achieve. Here we describe a rapid and reliable procedure for CYP2D6*4, *3, *6, and *9 genotyping. Design and methods Serum concentrations of venlafaxine and its pharmacologically active metabolite, O-desmethylvenlafaxine, were measured in patients treated with the antidepressant venlafaxine, a substrate of CYP2D6…

Volume flow in the common carotid artery does not decrease postprandially.

2003

Background and Purpose. A commonplace explanation for postprandial fatigue is the assumption of the redistribution of perfusion from the cerebral to the mesenterial territory. However, this assumption has never been scientifically proven. Methods. Because approximately 70% of the blood flow in the common carotid artery (CCA) is directed to the internal carotid artery, this vessel can be seen as a major brain-supplying artery. Flow volume in the CCA can be measured by color M-mode duplex sonography. The authors investigated the flow volume rate in 20 healthy volunteers before and after the intake of a high-energy meal. Heart rate, blood pressure, and expiratory CO2 were also measured at both…

Microduplications at 22q11.21 are associated with non-syndromic classic bladder exstrophy

2009

The exstrophy-epispadias complex (EEC) comprises a spectrum of urogenital anomalies in which part or all of the distal urinary tract fails to close. The present study aimed to identify microaberrations characterized by loss or gain of genomic material that contribute to the EEC at a genome-wide level. Molecular karyotyping, utilizing 549,839 single nucleotide polymorphisms (SNPs) with an average spacing of 5.7 kilobases, was performed to screen an initial cohort of 16 patients with non-syndromic EEC. A de novo microduplication involving chromosomal region 22q11.21 was identified in one patient with classic exstrophy of the bladder (CBE). Subsequent multiplex ligation-dependent probe amplifi…