An Evaluation of Performance and Coverage of Selected in Silico Metabolism Tools

Poster for ASCCT on Oct. 20-23, 2020 in RTP, NCScience Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25</p

Integrating an Analytical Methods and Mass Spectral Database with Cheminformatics Capabilities

Poster for Cheminformatics Resources of U.S. Governmental Organizations on October 18-20, 2023 in Silver Spring, MDScience Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25</p

table_2_High Incidence of Severe Combined Immunodeficiency Disease in Saudi Arabia Detected Through Combined T Cell Receptor Excision Circle and Next Generation Sequencing of Newborn Dried Blood Spots.PDF

<p>Severe combined immunodeficiency disease (SCID) is the most severe form of primary immunodeficiency disorders (PID). T-cell receptor excision circle (TREC) copy number analysis is an efficient tool for population-based newborn screening (NBS) for SCID and other T cell lymphopenias. We sought to assess the incidence of SCID among Saudi newborn population and examine the feasibility of using targeted next generation sequencing PID gene panel (T-NGS PID) on DNA isolated from dried blood spots (DBSs) in routine NBS programs as a mutation screening tool for samples with low TREC count. Punches from 8,718 DBS collected on Guthrie cards were processed anonymously for the TREC assay. DNA was extracted from samples with confirmed low TREC count, then screened for 22q11.2 deletion syndrome by real-time polymerase chain reaction and for mutations in PID-related genes by T-NGS PID panel. Detected mutations were confirmed by Sanger sequencing. Sixteen out of the 8,718 samples were confirmed to have low TREC copy number. Autosomal recessive mutations in AK2, JAK3, and MTHFD1 were confirmed in three samples. Two additional samples were positive for the 22q11.2 deletion syndrome. In this study, we provide evidence for high incidence of SCID among Saudi population (1/2,906 live births) and demonstrate the feasibility of using T-NGS PID panel on DNA extracted from DBSs as a new reliable, rapid, and cost-effective mutation screening method for newborns with low TREC assay, which can be implemented as part of NBS programs for SCID.</p

table_1_High Incidence of Severe Combined Immunodeficiency Disease in Saudi Arabia Detected Through Combined T Cell Receptor Excision Circle and Next Generation Sequencing of Newborn Dried Blood Spots.PDF

<p>Severe combined immunodeficiency disease (SCID) is the most severe form of primary immunodeficiency disorders (PID). T-cell receptor excision circle (TREC) copy number analysis is an efficient tool for population-based newborn screening (NBS) for SCID and other T cell lymphopenias. We sought to assess the incidence of SCID among Saudi newborn population and examine the feasibility of using targeted next generation sequencing PID gene panel (T-NGS PID) on DNA isolated from dried blood spots (DBSs) in routine NBS programs as a mutation screening tool for samples with low TREC count. Punches from 8,718 DBS collected on Guthrie cards were processed anonymously for the TREC assay. DNA was extracted from samples with confirmed low TREC count, then screened for 22q11.2 deletion syndrome by real-time polymerase chain reaction and for mutations in PID-related genes by T-NGS PID panel. Detected mutations were confirmed by Sanger sequencing. Sixteen out of the 8,718 samples were confirmed to have low TREC copy number. Autosomal recessive mutations in AK2, JAK3, and MTHFD1 were confirmed in three samples. Two additional samples were positive for the 22q11.2 deletion syndrome. In this study, we provide evidence for high incidence of SCID among Saudi population (1/2,906 live births) and demonstrate the feasibility of using T-NGS PID panel on DNA extracted from DBSs as a new reliable, rapid, and cost-effective mutation screening method for newborns with low TREC assay, which can be implemented as part of NBS programs for SCID.</p

A novel deletion of 2-bp nucleotides in the human <i>CYP27B1</i> gene.

<p>A homozygous deletion of AC nucleotides (c.934_935delAC) in exon 5 was found in a patient from family 7. A heterozygous deletion was found in both of his parents. The deletion results in a frameshift and creates a premature TGA stop codon 19 amino acids downstream from the frameshift (p.T312RfsX19).</p

<i>CYP27B1</i> mutations in Turkish population.

<p><i>CYP27B1</i> mutations in Turkish population.</p

Novel splice site mutations in the human <i>CYP27B1</i> gene.

<p>(A) Sequence analysis of genomic DNA from peripheral lymphocytes. A homozygous mutation at the splice donor site of intron 7 (c.1215+2T>A) were found in a patient from family 3. A homozygous silent SNV (c.1215 T>C) at the end of exon 7 was also identified. His parents carry a heterozygous mutation at both these locations, demonstrating they are in cis and not in trans. The mutations are indicated by arrows. (B) Sequence analysis of cDNA from patient’s peripheral lymphocytes. The mutation at the c.1215+2T>A leads to skipping of exon 7, resulting in exons 6 and 8 joined together.</p

Additional file 2: of Identification of a novel genetic locus underlying tremor and dystonia

Variants in candidate interval. (PDF 217 kb

Additional file 4: of Identification of a novel genetic locus underlying tremor and dystonia

CAMTA2 expression in brain. (PDF 1628 kb

Additional file 1: of A first-line diagnostic assay for limb-girdle muscular dystrophy and other myopathies

Clinical characteristics and biopsy results of index cases for families studied. (DOCX 223 kb