software program genequest  (DNASTAR)

Journal: Human Genome Variation

Article Title: Two novel mutations in the KHDC3L gene in Asian patients with recurrent hydatidiform mole

doi: 10.1038/hgv.2016.27

Figure Lengend Snippet: Chromatograms of the novel mutations in patients 1448 and 1335 and amplification refractory mutation system PCR (ARMS-PCR) gel electrophoresis result for c.17_20delGGTT mutation. ( a ) Sequence chromatograms showing the novel 4-bp deletion in the first exon of KHDC3L gene in patient 1448 (homozygous) and her paternal aunt (heterozygous) along with control subject with the normal sequence. ( b ) Agarose gel electrophoresis results of ARMS-PCR. Top panel shows the amplification of a 260-bp PCR product with mutant primers only in patient 1448 (lane 1) and not in six normal individuals (lanes 2–7). Lower panel shows the absence of PCR amplification with normal primers in patient 1448 (lane 1), but the amplification of a 264-bp product in normal individuals (lanes 2–7). The 100-bp DNA ladder is depicted on the right. ( c ) Sequence chromatogram showing the novel mutation affecting the donor splice site of KHDC3L intron 2 in patient 1335.

Article Snippet: The presence of three 4-bp deletions out of six known mutations in KHDC3L , which is a small gene (654 bp), is intriguing and raises questions about the presence of small direct and inverted repeats that could have mediated or promoted the occurrence of these deletions via a slipped-strand mispairing mechanism, as reported previously., We therefore used GeneQuest, a software program included in the LaserGene package (DNASTAR), and looked for short repeats within KHDC3L cDNA.

Techniques: Amplification, Mutagenesis, Nucleic Acid Electrophoresis, Sequencing, Agarose Gel Electrophoresis

Journal: Human Genome Variation

Article Title: Two novel mutations in the KHDC3L gene in Asian patients with recurrent hydatidiform mole

doi: 10.1038/hgv.2016.27

Figure Lengend Snippet: Schematic representation of KHDC3L protein structure and all identified mutations in patients with recurrent hydatidiform moles (RHMs). KH stands for K homology domain. Mutations found in patients with two defective alleles are in rectangles with continuous border. The dashed border rectangle corresponds to a single heterozygous variant found in one patient and not seen in controls. The c.17_20delGGTT and c.349+1G>A mutations were identified in the present study.

Article Snippet: The presence of three 4-bp deletions out of six known mutations in KHDC3L , which is a small gene (654 bp), is intriguing and raises questions about the presence of small direct and inverted repeats that could have mediated or promoted the occurrence of these deletions via a slipped-strand mispairing mechanism, as reported previously., We therefore used GeneQuest, a software program included in the LaserGene package (DNASTAR), and looked for short repeats within KHDC3L cDNA.

Techniques: Variant Assay

Journal: Human Genome Variation

Article Title: Two novel mutations in the KHDC3L gene in Asian patients with recurrent hydatidiform mole

doi: 10.1038/hgv.2016.27

Figure Lengend Snippet: Inverted, direct, and repeats identified in KHDC3L cDNA. ( a ) Distribution of inverted, direct, and tandem repeats along KHDC3L cDNA using GeneQuest (DNASTAR, Madison, WI) with the following parameters (a minimum number of 5-bp that are <50-bp apart) and Tandem Repeat Finder ( https://tandem.bu.edu/trf/trf.html ). An aqua box indicates an inverted repeat; a pink box indicates a direct repeat; and green boxes indicate tandem repeats. ( b ) Direct and inverted repeats flanking the 4-bp deletions in exons 1 and 2 are indicated by asterisks in ( a ) and brackets in ( b ). Inverted repeats flanking c.299_302delTCAA are indicated by brackets below exon 2 and those flanking c.322_325delGACT are indicated by brackets above exon 2.

Article Snippet: The presence of three 4-bp deletions out of six known mutations in KHDC3L , which is a small gene (654 bp), is intriguing and raises questions about the presence of small direct and inverted repeats that could have mediated or promoted the occurrence of these deletions via a slipped-strand mispairing mechanism, as reported previously., We therefore used GeneQuest, a software program included in the LaserGene package (DNASTAR), and looked for short repeats within KHDC3L cDNA.

Techniques:

Journal: Human Genome Variation

Article Title: Two novel mutations in the KHDC3L gene in Asian patients with recurrent hydatidiform mole

doi: 10.1038/hgv.2016.27

Figure Lengend Snippet: Recapitulation of the reproductive outcomes and ethnic origin of all described women with recessive KHDC3L mutations

Article Snippet: The presence of three 4-bp deletions out of six known mutations in KHDC3L , which is a small gene (654 bp), is intriguing and raises questions about the presence of small direct and inverted repeats that could have mediated or promoted the occurrence of these deletions via a slipped-strand mispairing mechanism, as reported previously., We therefore used GeneQuest, a software program included in the LaserGene package (DNASTAR), and looked for short repeats within KHDC3L cDNA.

Techniques: Mutagenesis

Journal: Journal of Clinical Microbiology

Article Title: Identification and Characterization of Variable-Number Tandem Repeats in the Yersinia pestis Genome

doi: 10.1128/jcm.39.9.3179-3185.2001

Figure Lengend Snippet: FIG. 1. Number of tandem repeat sequence arrays in the Y. pestis chromosome. Log of array numbers with repeat lengths from 1 to 21 bp detected by Genequest (black bars) and repeat lengths from 1 to 10 bp detected by the SSR program (gray bars) are presented. Larger repeat lengths of 22, 30, 36, 41, 45, 49, 115, 122, 123, 141, and 145 bp were observed but are not presented, as each was observed only once (ex- cept the 123-bp repeat length, which was observed three times).

Article Snippet: One approach employed the Genequest software program (Dnastar package; LaserGene, Inc., Madison, Wis.) direct repeat function set for the smallest scanning window size possible (8 nucleotides) to locate direct repeat arrays.

Techniques: Sequencing