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TABLE S2 List of mRNAs found in Staufen259-HA containing mRNPs Probe Set ID Gene Symbol Gene Title 217253_at --- (clone B3B3E13) Huntington's disease candidate region mRNA fragment 225440_at AGPAT3 1-acylglycerol-3-phosphate O-acyltransferase 3 228041_at AASDH 2-aminoadipic 6-semialdehyde dehydrogenase 232103_at BPNT1 3'(2'), 5'-bisphosphate nucleotidase 1 202539_s_at HMGCR 3-hydroxy-3-methylglutaryl-Coenzyme A reductase 233576_at HMGCLL1 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1 224986_s_at PDPK1 3-phosphoinositide dependent protein kinase-1 219708_at NT5M 5',3'-nucleotidase, mitochondrial 225814_at XRN1 5'-3' exoribonuclease 1 233632_s_at XRN1 5'-3' exoribonuclease 1 218786_at NT5DC3 5'-nucleotidase domain containing 3 205760_s_at OGG1 8-oxoguanine DNA glycosylase 202760_s_at AKAP2 A kinase (PRKA) anchor protein 2 /// PALM2-AKAP2 protein 235348_at ABHD13 abhydrolase domain containing 13 228490_at ABHD2 abhydrolase domain containing 2 63825_at ABHD2 abhydrolase domain containing 2 225098_at ABI2 abl interactor 2 212186_at ACACA acetyl-Coenzyme A carboxylase alpha 200965_s_at ABLIM1 actin binding LIM protein 1 242624_at ABLIM2 actin binding LIM protein family, member 2 226914_at ARPC5L actin related protein 2/3 complex, subunit 5-like 202422_s_at ACSL4 acyl-CoA synthetase long-chain family member 4 229725_at ACSL6 Acyl-CoA synthetase long-chain family member 6 234312_s_at ACSS2 acyl-CoA synthetase short-chain family member 2 219413_at ACBD4 acyl-Coenzyme A binding domain containing 4 213501_at ACOX1 acyl-Coenzyme A oxidase 1, palmitoyl 227962_at ACOX1 acyl-Coenzyme A oxidase 1, palmitoyl 227889_at AYTL1 acyltransferase like 1 209765_at ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 1552726_at ADAMTS17 ADAM metallopeptidase with thrombospondin type 1 motif, 17 1552727_s_at ADAMTS17 ADAM metallopeptidase with thrombospondin type 1 motif, 17 222516_at AP3M1 adaptor-related protein complex 3, mu 1 subunit 203410_at AP3M2 adaptor-related protein complex 3, mu 2 subunit 202398_at AP3S2 adaptor-related protein complex 3, sigma 2 subunit 235647_at AP4S1 Adaptor-related protein complex 4, sigma 1 subunit 207992_s_at AMPD3 adenosine monophosphate deaminase (isoform E) 212814_at KIAA0828 adenosylhomocysteinase 3 201196_s_at AMD1 adenosylmethionine decarboxylase 1 213245_at ADCY1 adenylate cyclase 1 (brain) 203741_s_at ADCY7 adenylate cyclase 7 212173_at AK2 adenylate kinase 2 224655_at AK3 adenylate kinase 3 225342_at AK3L1 adenylate kinase 3-like 1 201346_at ADIPOR2 adiponectin receptor 2 222518_at ARFGEF2 ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) 213433_at ARL3 ADP-ribosylation factor-like 3 202206_at ARL4C ADP-ribosylation factor-like 4C 202207_at ARL4C ADP-ribosylation factor-like 4C 242727_at ARL5B ADP-ribosylation factor-like 5B 217852_s_at ARL8B ADP-ribosylation factor-like 8B 225707_at ARL6IP6 ADP-ribosylation-like factor 6 interacting protein 6 225956_at LOC153222 adult retina protein 235556_at LOC153222 Adult retina protein 225229_at AFF4 AF4/FMR2 family, member 4 207016_s_at ALDH1A2 aldehyde dehydrogenase 1 family, member A2 221588_x_at ALDH6A1 aldehyde dehydrogenase 6 family, member A1 221589_s_at ALDH6A1 aldehyde dehydrogenase 6 family, member A1 221590_s_at ALDH6A1 Aldehyde dehydrogenase 6 family, member A1 205621_at ALKBH1 alkB, alkylation repair homolog 1 (E. coli) 225113_at AGPS alkylglycerone phosphate synthase 204976_s_at AMMECR1 Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region, gene 1 227021_at AOF1 amine oxidase (flavin containing) domain 1 225421_at ACY1L2 aminoacylase 1-like 2 202169_s_at AASDHPPT aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 226431_at ALS2CR13 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13 228255_at ALS2CR4 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4 241959_at ANAPC10 anaphase promoting complex subunit 10 /// similar to Anaphase-promoting complex subunit 10 (APC10) 235926_at ANAPC5 Anaphase promoting complex subunit 5 204742_s_at APRIN androgen-induced proliferation inhibitor 224900_at ANKFY1 ankyrin repeat and FYVE domain containing 1 218862_at ASB13 ankyrin repeat and SOCS box-containing 13 226861_at ASB8 ankyrin repeat and SOCS box-containing 8 238851_at ANKRD13A ankyrin repeat domain 13A 1556361_s_at ANKRD13C ankyrin repeat domain 13C 218418_s_at ANKRD25 ankyrin repeat domain 25 227064_at ANKRD40 ankyrin repeat domain 40 232600_at ANKRD42 Ankyrin repeat domain 42 230238_at ANKRD43 ankyrin repeat domain 43 220144_s_at ANKRD5 ankyrin repeat domain 5 225731_at ANKRD50 ankyrin repeat domain 50 219496_at ANKRD57 ankyrin repeat domain 57 227034_at ANKRD57 ankyrin repeat domain 57 218389_s_at APH1A anterior pharynx defective 1 homolog A (C. elegans) 224694_at ANTXR1 anthrax toxin receptor 1 201772_at AZIN1 antizyme inhibitor 1 212461_at AZIN1 antizyme inhibitor 1 240231_at AZIN1 Antizyme inhibitor 1 225522_at AAK1 AP2 associated kinase 1 201687_s_at API5 apoptosis inhibitor 5 228445_at AIFM2 apoptosis-inducing factor, mitochondrion-associated, 2 204859_s_at APAF1 apoptotic peptidase activating factor 1 225055_at AMZ2 Archaemetzincins-2 218185_s_at ARMC1 armadillo repeat containing 1 225283_at ARRDC4 arrestin domain containing 4 202820_at AHR aryl hydrocarbon receptor 223586_at ARNTL2 aryl hydrocarbon receptor nuclear translocator-like 2 229354_at AHRR aryl-hydrocarbon receptor repressor 203427_at ASF1A ASF1 anti-silencing function 1 homolog A (S. cerevisiae) 1552304_at ALG10 asparagine-linked glycosylation 10 homolog (yeast, alpha-1,2-glucosyltransferase) 227015_at ASPHD2 aspartate beta-hydroxylase domain containing 2 243477_at ATG10 ATG10 autophagy related 10 homolog (S. cerevisiae) 224728_at ATPAF1 ATP synthase mitochondrial F1 complex assembly factor 1 228168_at ATP5G3 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9) 237400_at ATP5S ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B) 238799_at ATP5S ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B) 204499_at AGTPBP1 ATP/GTP binding protein 1 223339_at ATPIF1 ATPase inhibitory factor 1 212297_at ATP13A3 ATPase type 13A3 212361_s_at ATP2A2 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 212135_s_at ATP2B4 ATPase, Ca++ transporting, plasma membrane 4 212136_at ATP2B4 ATPase, Ca++ transporting, plasma membrane 4 212062_at ATP9A ATPase, Class II, type 9A 226463_at ATP6V1C1 ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 203066_at GALNAC4S-6ST B cell RAG associated protein 239944_at BIRC1 Baculoviral IAP repeat-containing 1 225859_at BIRC4 baculoviral IAP repeat-containing 4 218471_s_at BBS1 Bardet-Biedl syndrome 1 225976_at BTF3L4 basic transcription factor 3-like 4 233255_s_at BIVM basic, immunoglobulin-like variable motif containing 218792_s_at BSPRY B-box and SPRY domain containing 202984_s_at BAG5 BCL2-associated athanogene 5 212312_at BCL2L1 BCL2-like 1 /// BCL2-like 1 1558143_a_at BCL2L11 BCL2-like 11 (apoptosis facilitator) 209311_at BCL2L2 BCL2-like 2 219521_at B3GAT1 beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P) 222462_s_at BACE1 beta-site APP-cleaving enzyme 1 201032_at BLCAP bladder cancer associated protein 241644_at BOLA2 bolA homolog 2 (E. coli) 213578_at BMPR1A bone morphogenetic protein receptor, type IA 218024_at BRP44L brain protein 44-like 225285_at BCAT1 branched chain aminotransferase 1, cytosolic 243302_at BCKDHB Branched chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease) 213473_at BRAP BRCA1 associated protein 228787_s_at BCAS4 breast carcinoma amplified sequence 4 231810_at BRI3BP BRI3 binding protein 225446_at BRWD1 bromodomain and WD repeat domain containing 1 235727_at BTBD5 BTB (POZ) domain containing 5 224945_at BTBD7 BTB (POZ) domain containing 7 235248_at BTBD9 BTB (POZ) domain containing 9 205299_s_at BTN2A2 butyrophilin, subfamily 2, member A2 201131_s_at CDH1 cadherin 1, type 1, E-cadherin (epithelial) 214665_s_at CHP calcium binding protein P22 228555_at CAMK2D Calcium/calmodulin-dependent protein kinase (CaM kinase) II delta 230706_s_at CAMK2N2 calcium/calmodulin-dependent protein kinase II inhibitor 2 225759_x_at CLMN calmin (calponin-like, transmembrane) 200623_s_at CALM3 calmodulin 3 (phosphorylase kinase, delta) 212710_at CAMSAP1 calmodulin regulated spectrin-associated protein 1 232012_at CAPN1 calpain 1, (mu/I) large subunit 212345_s_at CREB3L2 cAMP responsive element binding protein 3-like 2 201989_s_at CREBL2 cAMP responsive element binding protein-like 2 201990_s_at CREBL2 cAMP responsive element binding protein-like 2 228323_at CASC5 cancer susceptibility candidate 5 226368_at CHST11 Carbohydrate (chondroitin 4) sulfotransferase 11 226372_at CHST11 Carbohydrate (chondroitin 4) sulfotransferase 11 223786_at CHST6 carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6 214082_at CA5B carbonic anhydrase VB, mitochondrial 201941_at CPD carboxypeptidase D 232198_at CRLS1 Cardiolipin synthase 1 241741_at CRLS1 cardiolipin synthase 1 203633_at CPT1A carnitine palmitoyltransferase 1A (liver) 226656_at CRTAP cartilage associated protein 225231_at CBL Cas-Br-M (murine) ecotropic retroviral transforming sequence 229010_at CBL Cas-Br-M (murine) ecotropic retroviral transforming sequence 208865_at CSNK1A1 casein kinase 1, alpha 1 208866_at CSNK1A1 casein kinase 1, alpha 1 242486_at CSNK1G1 Casein kinase 1, gamma 1 212073_at CSNK2A1 casein kinase 2, alpha 1 polypeptide /// casein
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  • Identification and Analysis of Single-Nucleotide Polymorphisms in the Gemcitabine Pharmacologic Pathway

    Identification and Analysis of Single-Nucleotide Polymorphisms in the Gemcitabine Pharmacologic Pathway

    The Pharmacogenomics Journal (2004) 4, 307–314 & 2004 Nature Publishing Group All rights reserved 1470-269X/04 $30.00 www.nature.com/tpj ORIGINAL ARTICLE Identification and analysis of single-nucleotide polymorphisms in the gemcitabine pharmacologic pathway AK Fukunaga1 ABSTRACT 2 Significant variability in the antitumor efficacy and systemic toxicity of S Marsh gemcitabine has been observed in cancer patients. However, there are 1 DJ Murry currently no tools for prospective identification of patients at risk for TD Hurley3 untoward events. This study has identified and validated single-nucleotide HL McLeod2 polymorphisms (SNP) in genes involved in gemcitabine metabolism and transport. Database mining was conducted to identify SNPs in 14 genes 1Department of Clinical Pharmacy and Pharmacy involved in gemcitabine metabolism. Pyrosequencing was utilized to Practice, Purdue University, W. Lafayette, IN, determine the SNP allele frequencies in genomic DNA from European and 2 USA; Departments of Medicine, Genetics, and African populations (n ¼ 190). A total of 14 genetic variants (including 12 Molecular Biology and Pharmacology, Washington University School of Medicine and SNPs) were identified in eight of the gemcitabine metabolic pathway genes. the Siteman Cancer Center, St Louis, MO, USA; The majority of the database variants were observed in population samples. 3Department of Biochemistry and Molecular Nine of the 14 (64%) polymorphisms analyzed have allele frequencies that Biology, Indiana University School of Medicine, were found to be significantly different between the European and African Indianapolis, IN, USA populations (Po0.05). This study provides the first step to identify markers Correspondence: for predicting variability in gemcitabine response and toxicity. Dr HL McLeod, Washington University The Pharmacogenomics Journal (2004) 4, 307–314.
  • A Dominant Mutation in RPE65 Identified by Whole-Exome

    A Dominant Mutation in RPE65 Identified by Whole-Exome

    A Dominant Mutation in RPE65 Identified by Whole-Exome Sequencing Causes Retinitis Pigmentosa with Choroidal Involvement Peter Humphries, Sara J Bowne, Marian M Humphries, Lori S Sullivan, Paul F Kenna, Lawrence Cs Tam, Anna-Sophia Kiang, Matthew Campbell, George M Weinstock, Daniel C Koboldt, et al. To cite this version: Peter Humphries, Sara J Bowne, Marian M Humphries, Lori S Sullivan, Paul F Kenna, et al.. A Dominant Mutation in RPE65 Identified by Whole-Exome Sequencing Causes Retinitis Pigmentosa with Choroidal Involvement. European Journal of Human Genetics, Nature Publishing Group, 2011, 10.1038/ejhg.2011.86. hal-00649449 HAL Id: hal-00649449 https://hal.archives-ouvertes.fr/hal-00649449 Submitted on 8 Dec 2011 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Edited manuscript for European Journal of Human Genetics April 4th 2011. “A Dominant Mutation in RPE65 Identified by Whole-Exome Sequencing Causes Retinitis Pigmentosa with Choroidal Involvement” Sara J. Bowne1*, Marian M. Humphries2*, Lori S. Sullivan1*, Paul F. Kenna2,3*, Lawrence C.S. Tam2, Anna Sophia Kiang2, Matthew Campbell2, George M. Weinstock4, Daniel C. Koboldt4, Li Ding4, Robert S. Fulton4, Erica J. Sodergren4, Denis Alman2, Sophia Millington-Ward2, Arpad Palfi2, Alex McKee2, Susan H.