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Report for Clinical Trial NCT01016106

Developed by Shray Alag, 2020.
SNP Clinical Trial Gene

Genetic Screening for Filaggrin Mutation in Atopic Dermatitis and Ichthyosis Vulgaris in the African American Population

The investigators' primary objective is to identify common and rare mutations in the filaggrin gene in African American patients with a diagnosis of atopic dermatitis and ichthyosis vulgaris. Atopic dermatitis, or eczema, is a common, chronic, relapsing and remitting problem in many children and affects 10-20% of the pediatric population. Itch is a predominant feature of this disease and is quite disruptive to daily activities of life. In addition to itch, it is characterized by markedly dry skin, small red bumps that may have fluid. Ichthyosis vulgaris is characterized by extremely dry, scaly skin with a fine white scale and increased amounts of lines noted on the palms. Filaggrin is a protein that is essential for the skin to function properly as a barrier and found to be mutated in some European patients with ichthyosis vulgaris and atopic dermatitis. This association has not been looked at in the African American population. Genomic DNA (gDNA) will be purified from buccal swabs using commercially available kits and analyzed.

NCT01016106 Atopic Dermatitis Ichthyosis Vulgaris
MeSH:Dermatitis, Atopic Ichthyosis Ichthyosis, Lamellar Ichthyosis Vulgaris Dermatitis Eczema
HPO:Atopic dermatitis Congenital nonbullous ichthyosiform erythroderma Eczema Eczematoid dermatitis Ichthyosis Inflammatory abnormality of the skin

1 Interventions

Name: Buccal Swab

Description: During a single visit, a subject data collection form will be completed and DNA will be extracted from samples (buccal swabs) and then analyzed at IBT laboratories in Lenexa, Kansas.
Type: Genetic
Group Labels: 2

AA patients (controls) AA pts AD and IV


Primary Outcomes

Description: Buccal swab samples were obtained from each subject. Deoxyribonucleic acid (DNA) was purified from buccal swabs (IsoHelix Swabs, BocaScientific, Boca Raton, FL) and quantified by ultraviolet spectrophotometry. Purified genomic DNA and controls were amplified by polymerase chain reaction (PCR) from three different regions of FLG exon 3 with three primer sets. PCR products were analyzed by electrophoresis, purified (Qiaquick, Qiagen, Valencia, CA), and subjected to duplicate cycle sequencing reactions using ABI BigDye v3.1 reagents (Applied Biosystems, Carlsbad, CA). Labeled sequencing products were purified for capillary electrophoresis (ABI3730 or ABI3130 sequencer with POP7 polymer), and sequence results were examined using ABI SeqScape software. All nucleotide changes were noted, including 30 single nucleotide polymorphism (SNPs) in the population tested, the most common of which were coding changes at T454A, H2507Q, and G2545R, and silent change at nucleotide t2508c.

Measure: Heterozygous for Filaggrin (FLG) Null Mutations

Time: 1 month

Purpose: Diagnostic

Allocation: Non-Randomized

Single Group Assignment


There are 3 SNPs

SNPs


1 G2545R

All nucleotide changes were noted, including 30 single nucleotide polymorphism (SNPs) in the population tested, the most common of which were coding changes at T454A, H2507Q, and G2545R, and silent change at nucleotide t2508c.. Inclusion Criteria: - Age greater than 6 months - Affected subjects: Must be African American and have a diagnosis of both atopic dermatitis or eczema as well as ichthyosis vulgaris - Control subjects: Must be healthy African American subjects - Must be willing to not apply emollients for 24 hours prior to visit. --- T454A --- --- H2507Q --- --- G2545R ---


2 H2507Q

All nucleotide changes were noted, including 30 single nucleotide polymorphism (SNPs) in the population tested, the most common of which were coding changes at T454A, H2507Q, and G2545R, and silent change at nucleotide t2508c.. Inclusion Criteria: - Age greater than 6 months - Affected subjects: Must be African American and have a diagnosis of both atopic dermatitis or eczema as well as ichthyosis vulgaris - Control subjects: Must be healthy African American subjects - Must be willing to not apply emollients for 24 hours prior to visit. --- T454A --- --- H2507Q ---


3 T454A

All nucleotide changes were noted, including 30 single nucleotide polymorphism (SNPs) in the population tested, the most common of which were coding changes at T454A, H2507Q, and G2545R, and silent change at nucleotide t2508c.. Inclusion Criteria: - Age greater than 6 months - Affected subjects: Must be African American and have a diagnosis of both atopic dermatitis or eczema as well as ichthyosis vulgaris - Control subjects: Must be healthy African American subjects - Must be willing to not apply emollients for 24 hours prior to visit. --- T454A ---



HPO Nodes


HPO:
HP:0011123: Inflammatory abnormality of the skin
Genes 462
MEFV IL2RG NCF4 EPG5 TRAF3IP2 ABCA12 KRT17 IL2RG COL1A1 IL17RC HLCS GPR101 B2M TNFRSF1B DCLRE1C KRT14 KDF1 PIK3CA PAH LYZ NOD2 CLEC7A IL12A SDHC TP63 FLT4 LAMC2 PRKACA CHD7 FOXP3 NCSTN SMARCC2 HSPA9 LACC1 DSE RNU4ATAC IRAK1 IL12A-AS1 ERAP1 RAC1 IL7R IL17RA IL10RB CHST14 ADA DNASE1L3 CTSC TBX1 ESR1 DNAJC21 PRMT7 IL4R ERCC5 MTHFD1 NIPAL4 ANK1 CERS3 GINS1 UROS TEK UFD1 MYSM1 NCF2 VEGFC TGM1 TNFRSF1B DCLRE1C RMRP CARD14 RBCK1 CACNA1G DSG1 SPINK5 JMJD1C MEIS2 EBP UBE2A RAG2 FAT4 SRD5A3 FCGR2A WAS MEFV POMP POR PAPSS2 CCBE1 FCGR2B HLA-DRB1 RTTN NCF1 DCLRE1C NIPAL4 KANSL1 MS4A2 STAT3 IL7 STAT3 MNX1 SEC24C KRT10 ADA2 C1R GFI1 CIB1 ADAMTS3 MBL2 MSMO1 SLCO2A1 GJA1 KRT10 GJC2 LAMA3 TRAF6 PEPD SUOX HLA-DPA1 STAT4 NAXD KRT1 NEK9 SHOC2 COL5A2 TNFRSF1A IL1RN TBCK PSENEN BTD ESR1 BTK ABCA12 RAC1 COMT ERCC3 MVK MVK STAT1 SBDS LIPN NFKB2 WAS NFKB1 WNT4 NLRP12 NFKB2 AK2 GLUL RNF113A SULT2B1 FLG TNFRSF1A GATA1 CDK10 ZNF750 PCCA PSMB4 DNASE1 KRT1 NOD2 COL7A1 BTK SLC6A19 TBX1 LIG4 SMARCA2 ACADVL RAG1 RIPK1 ERCC2 IL36RN PTPN22 KIT HYOU1 HPGD C1QA CLEC7A RAG2 DNAJC21 CYBB KRT16 RREB1 SMARCA2 ELANE ALOX12B ERCC4 PGM3 HLA-DRB1 CCR1 AP1B1 MPDU1 ERCC2 GJB4 NSUN2 CYP4F22 PEPD FOXP3 CD3E SPINK5 KIT PIGA APOA1 GP1BB CTSB EFL1 COX4I2 SH3PXD2B STING1 TRPM1 ERCC3 CD3D WIPF1 CTLA4 BCL11B NSUN2 TGFB1 CYBC1 WAS GJB2 HPGD STAT3 IL7R SP110 CTLA4 PRTN3 GJC2 ALOXE3 HLCS FERMT3 ITGA6 IRF2BP2 KRT1 GTF2H5 FGA MIF GNA11 TNFAIP3 JAK3 TP63 LPIN2 CD247 DOCK8 MBTPS2 TRAF3IP2 HLA-DRB1 FLI1 NFE2L2 LPIN2 FOXC2 EDARADD KLRC4 ZAP70 CD3G PNPLA1 CARMIL2 ENPP1 H6PD LRRC8A ABCA12 FGFR2 MYSM1 USP8 SLC29A3 LAMB3 SDR9C7 SPTB GATA3 PSTPIP1 CD79B LBR SRP54 SRP54 TAF1 SPTA1 GJB3 HLA-C IKBKG ABCC6 IL7R KIF11 RFX5 TKT IL17RA PSEN1 HIRA NCF2 CASR CARD9 LIG4 CCBE1 ELANE SHANK3 CASP8 CARD11 CD79A NOD2 GJB2 KRT9 KDF1 SMARCAD1 PDGFRA BLNK PSMB9 RFXAP TCF3 FECH C5 CTSC HLA-B CD28 DHCR7 PCCB CTLA4 HLA-DPB1 HSD3B2 AUTS2 PGM3 POLE CSTA AP1S3 BRAF LMBRD1 ADA EGFR MBTPS2 NCF4 GTF2E2 STAT1 CFI RFXANK TMC8 ITGB4 MSN C4A RFXANK UBAC2 KDSR TGM1 NLRP3 CD28 SIK3 MBTPS2 SH3PXD2B PNPLA1 ERCC2 CIITA IL23R WNT4 RFXAP RAG2 NLRC4 HLA-B BTK KRT1 IL2RG NCF1 SLC4A1 CASP10 LMBRD1 GTF2H5 TARS1 PIK3R1 PAH CHST14 RBP4 RBM8A CTLA4 TLR4 CDH23 CYP4F22 GJB2 ALOXE3 SDHB LBR IL10 GJB6 MPLKIP RAG1 ALOX12B DDX41 KRT10 RAG1 SDHA XIAP TFRC NIPAL4 AIP MORC2 EXTL3 STAT4 IL10RA PSMB8 ARVCF SLC39A4 EPB42 ZAP70 RNU4ATAC POLR3A IL2RA PTPN22 IL17F AGA TGM5 SLC30A2 COL5A1 TREX1 TMC6 BTNL2 CYBA EDAR TGM1 CYBA RFX5 LHCGR TBX1 NSMCE3 BTNL2 FAM111B AIRE NR3C1 HDAC4 CARD14 LYST LIG4 MCCC2 ECM1 TGM1 PLA2G7 TCIRG1 LYST KIT FLI1 IL17F CTLA4 FAS KRT5 FERMT1 ZNF341 CIITA MYD88 PSTPIP1 XYLT1 ADAM17 SPP1 HLA-DQB1 HPGD AIRE CYBB EDA TTC7A TTC7A NLRP3 IGHM PTPRC FOXP1 IGLL1 IL6 BTD DOCK8 FECH IFIH1 KRT5 WIPF1
Protein Mutations 4
G2545R H2507Q T454A V66M
SNP 1
rs6265