Journal: European Journal of Human Genetics

Article Title: An 8.9 Mb 19p13 duplication associated with precocious puberty and a sporadic 3.9 Mb 2q23.3q24.1 deletion containing NR4A2 in mentally retarded members of a family with an intrachromosomal 19p-into-19q between-arm insertion

doi: 10.1038/ejhg.2008.261

Figure Lengend Snippet: Array-CGH and SNP-chip-based copy number analyses of the proband. A subtelomeric 19p duplication was detected by 1 Mb CytoChip BAC array-CGH analysis, as indicated by the green line (a). The 19p duplication was subsequently fine mapped by Affymetrix 250 K SNP-chip copy number analysis (marked by blue boxes; b), and Agilent 244 K oligo array-CGH analysis (marked by a green line; c), both placing the 19p-duplication distal to the GPR54 gene. In all, 850-band chromosome ideograms are shown below the array profiles.

Article Snippet: The following array-CGH analyses were carried out according to the suppliers' instructions: the CytoChip Reference Manual Version 0.10 (BlueGnome), the Oligonucleotide Array-based CGH for Genomic DNA Analysis Protocol v5.0. (Agilent Technologies) and the GeneChip Human Mapping 500 K Assay Manual (Affymetix).

Techniques:

Journal: BMC Bioinformatics

Article Title: SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data

doi: 10.1186/1471-2105-10-121

Figure Lengend Snippet: Flowcharts of data processing for pair-wise linkage analysis employing MLINK or Superlink by SNP HiTLink . In Windows OS, import of SNP data, generation of allele frequency file, annotation file and lkin file are conducted along with selection of markers. After lkin file is transported to Unix OS, run_linkage.pl carries out continuous run of MLINK or Superlink by rewriting pedin.pre and pedin.dat files for each marker.

Article Snippet: Allegro is available from deCODE genetics, Inc. At present, SNP HiTLink accepts files in the CHP file format (filename.chp) of the Affymetrix Mapping 100 k/500 k array set and Genome-Wide Human SNP array 5.0/6.0.

Techniques: Selection, Marker

Journal: BMC Bioinformatics

Article Title: SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data

doi: 10.1186/1471-2105-10-121

Figure Lengend Snippet: Flowcharts of data processing for multipoint linkage analysis employing Merlin or Allegro with SNP HiTLink . Procedures are basically similar to those by pair-wise analysis except that the model setting, selection of intermarker distances are executable here. run_linkage.pl carries out a run of Allegro or Merlin with all selected markers by writing whole information in pedin.pre, datain.dat.

Article Snippet: Allegro is available from deCODE genetics, Inc. At present, SNP HiTLink accepts files in the CHP file format (filename.chp) of the Affymetrix Mapping 100 k/500 k array set and Genome-Wide Human SNP array 5.0/6.0.

Techniques: Selection

Journal: BMC Bioinformatics

Article Title: SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data

doi: 10.1186/1471-2105-10-121

Figure Lengend Snippet: Interface of first step of "build lkin file"(a) and "option settings"(b) of SNP HiTLink .

Article Snippet: Allegro is available from deCODE genetics, Inc. At present, SNP HiTLink accepts files in the CHP file format (filename.chp) of the Affymetrix Mapping 100 k/500 k array set and Genome-Wide Human SNP array 5.0/6.0.

Techniques:

Journal: Nature Communications

Article Title: Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment

doi: 10.1038/s41467-024-48124-4

Figure Lengend Snippet: a IGV genome browser image in Nalm6 cells showing the genomic context, chromatin accessibility, and EIF3A promoter connectivity using promoter CHiC of the top functional regulatory variant, rs1247117, with the highest allele-specific MPRA activity. Genomic binding profiles are also shown for RNA polymerase II (RNA Pol2), histone H3 lysine 27 acetylation (H3K27Ac), and PU.1. b rs1247117 lies in a PU.1 binding motif. The human genome reference sequence, Nalm6 genome sequence, location of rs1247117, and PU.1 position weight matrix are shown. c Design of biotinylated DNA probes for in vitro rs1247117 pulldown. d Biotinylated DNA pulldown shows rs1247117 allele-dependent enrichment of PU.1 binding. Blot shown is representative of two independent experiments. Densitometric quantification of two blots is shown. e CRISPR/Cas9 was used to change the allele at rs1247117 from A > G in Nalm6 cells. Data show the location of gRNA and ssODN, as well as NGS reads obtained from clone 1 and 2 at rs1247117. f PU.1 ChIP-PCR shows increased PU.1 binding at the rs1247117 locus using two A > G modified clones and 3 primer sets. Data shown are mean ± SD of three independent experiments for each primer set. Two-way ANOVA with Dunnett’s multiple comparisons correction, n = 3. g ATAC-seq data normalized for frequency of reads in peaks (FRIP) show a significantly higher count of G nucleotides in two clones of A > G modified Nalm6 cells compared to the count of A nucleotides detected in parental Nalm6 cells. Data shown are the mean ± SD. Bonferroni corrected, two-tailed Student’s T tests, n = 3. h Western blots and quantification showing decreased EIF3A expression in A > G modified Nalm6 cells. Blots shown are representative of three independent experiments. Quantification data shown are the mean ± SD. Two-tailed Student’s T tests compare parental Nalm6 to combined data from A > G clones, n = 3. All source data and statistical parameters are provided in the Source Data file.

Article Snippet: Briefly, genomic DNA was collected from primary ALL cells of patients enrolled on TOTXV and TOTXVI protocols using Blood and Cell Culture DNA kit (Qiagen), and SNP genotyping was performed using the Affymetrix Gene ChIP Human Mapping 500 K array or Affymetrix Genome-Wide Human SNP 6.0 array.

Techniques: Functional Assay, Variant Assay, Activity Assay, Binding Assay, Sequencing, In Vitro, CRISPR, Modification, Clone Assay, Two Tailed Test, Western Blot, Expressing