Genes differentially expressed between normal, MGUS, and myeloma samples that are in regions of LOH present in 10% of samples as identified in Table S1
. | . | . | . | Normal vs. MGUS . | . | Normal vs. MM . | . | MGUS vs. MM . | . | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome . | HGNC symbol . | Description . | NCBI accession no. . | Fold change . | P . | Fold change . | P . | Fold change . | P . | |||
| 1p13.3 | KCND3 | Potassium voltage-gated channel, Shal related subfamily, member 3 | AF048713 | 1.99 | .003 | 1.74 | .002 | – | – | |||
| 1p13-p12 | HMGCS2 | 3-Hydroxy-3-methylglutaryl-coenzyme A synthase 2 (mitochondrial) | X83618 | – | – | –2.22 | .036 | –1.52 | .032 | |||
| 1p31.1 | ACADM | Acyl-coenzyme A dehydrogenase, C-4 to C-12 straight chain | M91432 | – | – | – | – | –1.8 | .040 | |||
| 4p16.1 | WDR1 | WD repeat domain 1 | AL050108 | – | – | – | – | –2.07 | .009 | |||
| 5q31 | SEPP1 | Selenoprotein P, plasma, 1 | Z11793 | –6.2 | .027 | –10.04 | .021 | – | – | |||
| 6p21.33 | HIST1H2BK | Histone 1, H2bk | AJ223352 | –3.24 | .007 | – | – | 2.14 | .020 | |||
| 6p22-p21.3 | HIST1H1B | Histone 1, H1b | Z98744 | – | – | 2.82 | .020 | – | – | |||
| 6q12 | PTP4A1 | Protein tyrosine phosphatase type IVA, member 1 | U48296 | –2.68 | .031 | –3.2 | .021 | – | – | |||
| 6q22-q23 | MYB | v-myb myeloblastosis viral oncogene homolog (avian) | U22376 | 2.16 | .028 | 2.53 | .005 | – | – | |||
| 6q25.1 | ESR1 | Estrogen receptor 1 | X03635 | – | – | 1.75 | .035 | – | – | |||
| 6q25-q27 | WTAP | Wilms tumor 1 associated protein | D14661 | – | – | –3.06 | .026 | – | – | |||
| 8p12 | TMEM66 | Transmembrane protein 66 | W26659 | – | – | –2.25 | .007 | – | – | |||
| 8p21.3 | DOK2 | Docking protein 2, 56 kDa | AF034970 | – | – | 4.07 | .009 | – | – | |||
| 8p21.3 | GFRA2 | GDNF family receptor α 2 | U97145 | –3.22 | .047 | – | – | – | – | |||
| 8p22-21.3 | ASAH1 | N-acylsphingosine amidohydrolase (acid ceramidase) 1 | U70063 | – | – | –2.72 | .018 | – | – | |||
| 12p13.2 | GABARA PL1 | GABA(A) receptor-associated protein-like 1 | W28281 | – | – | –3.13 | .043 | – | – | |||
| 12q23.3 | CKAP4 | Cytoskeleton-associated protein 4 | X69910 | –2.45 | .029 | –2.47 | .028 | – | – | |||
| 13q12 | HMGB1 | High-mobility group box 1 | D63874 | – | – | –3.15 | .030 | – | – | |||
| 13q12.1 | SAP18 | Sin3-associated polypeptide, 18 kDa | U96915 | – | – | –4.41 | .042 | – | – | |||
| 13q12.3-q1 3.1 | GTF3A | General transcription factor IIIA | D32257 | –2.81 | .045 | –3.2 | .036 | – | – | |||
| 13q12-q13 | CG018 | Hypothetical gene CG018 | AL049786 | 1.74 | .011 | – | – | – | – | |||
| 13q12-q14 | TPT1 | Tumor protein, translationally controlled 1 | X16064 | – | – | –1.55 | <.001 | – | – | |||
| 13q14.11 | MRPS31 | Mitochondrial ribosomal protein S31 | Z68747 | – | – | –3.21 | .010 | – | – | |||
| 13q31.2-q3 2.3 | STK24 | Serine/threonine kinase 24 (STE20 homolog, yeast) | AF024636 | –3.31 | .004 | –4.57 | .004 | – | – | |||
| 13q32 | ZIC2 | Zic family member 2 (odd-paired homolog, Drosophila) | AF104902 | – | – | 1.31 | .008 | – | – | |||
| 13q32.3 | TM9SF2 | Transmembrane 9 superfamily member 2 | U81006 | –3.23 | .020 | –4.28 | .013 | – | – | |||
| 13q34 | ATP11A | ATPase, class VI, type 11A | AB028944 | 2.34 | .001 | 1.96 | .003 | – | – | |||
| 13q34 | LAMP1 | Lysosomal-associated membrane protein 1 | J04182 | –2.9 | .013 | –4.47 | .008 | – | – | |||
| 14q22-q24 | ZFP36L1 | Zinc finger protein 36, C3H type-like 1 | X79067 | –5.6 | .006 | –7.45 | .004 | – | – | |||
| 14q24.1 | ACTN1 | Actinin, α 1 | X15804 | – | – | – | – | –23.19 | .046 | |||
| 16q12.2-q13 | HERPUD1 | Endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 | D14695 | –1.99 | .013 | –2.94 | <.001 | – | – | |||
| 16q13 | CNGB1 | Cyclic nucleotide gated channel β 1 | U18945 | 2.92 | <.001 | 2.84 | .002 | – | – | |||
| 16q22.3q24.1 | GABARAPL2 | GABA(A) receptor-associated protein-like 2 | AI565760 | –2.44 | .042 | –2.92 | .027 | – | – | |||
| 16q22-q23 | MAF | v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) | AF055376 | – | – | –9.81 | .049 | – | – | |||
| 16q24.2 | MAP1LC3B | Microtubule-associated protein 1 light chain 3 β | W28807 | –2.12 | .031 | –3.53 | .008 | – | – | |||
| 16q24.3 | RPL13 | Ribosomal protein L13 | X64707 | – | – | – | – | 1.5 | .043 | |||
| 17p13.1 | GABARAP | GABA(A) receptor-associated protein | AF044671 | –2.52 | .031 | –3.26 | .020 | – | – | |||
| 17p13.1 | SENP3 | SUMO1/sentrin/SMT3 specific protease 3 | AL050283 | – | – | 2.04 | .041 | – | – | |||
| 17p13.1 | CD68 | Serine/threonine kinase 17b (apoptosis-inducing) | AA203487 | – | – | – | – | –2.02 | .009 | |||
| 20p12 | BMP2 | Bone morphogenetic protein 2 | M22489 | – | – | 85.74 | .002 | 10.71 | .039 | |||
| 20p12.1 | DSTN | Destrin (actin depolymerizing factor) | S65738 | – | – | –2.54 | .005 | – | – | |||
| 20p13 | SOX12 | SRY (sex determining region Y)-box 12 | U35612 | 1.62 | .017 | 1.98 | .004 | – | – | |||
| 20pter-p12 | PRNP | Prion protein | U29185 | –3.86 | .006 | –5.12 | .005 | – | – | |||
| 22q12.1 | TPST2 | Tyrosylprotein sulfotransferase 2 | AF049891 | –4.02 | .014 | –6.72 | .011 | – | – | |||
| 22q12.1 | XBP1 | X-box binding protein 1 | Z93930 | – | – | –1.72 | .002 | – | – | |||
| 22q13.1 | TOM1 | Target of myb1 (chicken) | AJ006973 | 3.07 | .009 | – | – | – | – | |||
| 22q13.31 | KIAA0153 | KIAA0153 protein | D63487 | – | – | 1.72 | .006 | – | – | |||
. | . | . | . | Normal vs. MGUS . | . | Normal vs. MM . | . | MGUS vs. MM . | . | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome . | HGNC symbol . | Description . | NCBI accession no. . | Fold change . | P . | Fold change . | P . | Fold change . | P . | |||
| 1p13.3 | KCND3 | Potassium voltage-gated channel, Shal related subfamily, member 3 | AF048713 | 1.99 | .003 | 1.74 | .002 | – | – | |||
| 1p13-p12 | HMGCS2 | 3-Hydroxy-3-methylglutaryl-coenzyme A synthase 2 (mitochondrial) | X83618 | – | – | –2.22 | .036 | –1.52 | .032 | |||
| 1p31.1 | ACADM | Acyl-coenzyme A dehydrogenase, C-4 to C-12 straight chain | M91432 | – | – | – | – | –1.8 | .040 | |||
| 4p16.1 | WDR1 | WD repeat domain 1 | AL050108 | – | – | – | – | –2.07 | .009 | |||
| 5q31 | SEPP1 | Selenoprotein P, plasma, 1 | Z11793 | –6.2 | .027 | –10.04 | .021 | – | – | |||
| 6p21.33 | HIST1H2BK | Histone 1, H2bk | AJ223352 | –3.24 | .007 | – | – | 2.14 | .020 | |||
| 6p22-p21.3 | HIST1H1B | Histone 1, H1b | Z98744 | – | – | 2.82 | .020 | – | – | |||
| 6q12 | PTP4A1 | Protein tyrosine phosphatase type IVA, member 1 | U48296 | –2.68 | .031 | –3.2 | .021 | – | – | |||
| 6q22-q23 | MYB | v-myb myeloblastosis viral oncogene homolog (avian) | U22376 | 2.16 | .028 | 2.53 | .005 | – | – | |||
| 6q25.1 | ESR1 | Estrogen receptor 1 | X03635 | – | – | 1.75 | .035 | – | – | |||
| 6q25-q27 | WTAP | Wilms tumor 1 associated protein | D14661 | – | – | –3.06 | .026 | – | – | |||
| 8p12 | TMEM66 | Transmembrane protein 66 | W26659 | – | – | –2.25 | .007 | – | – | |||
| 8p21.3 | DOK2 | Docking protein 2, 56 kDa | AF034970 | – | – | 4.07 | .009 | – | – | |||
| 8p21.3 | GFRA2 | GDNF family receptor α 2 | U97145 | –3.22 | .047 | – | – | – | – | |||
| 8p22-21.3 | ASAH1 | N-acylsphingosine amidohydrolase (acid ceramidase) 1 | U70063 | – | – | –2.72 | .018 | – | – | |||
| 12p13.2 | GABARA PL1 | GABA(A) receptor-associated protein-like 1 | W28281 | – | – | –3.13 | .043 | – | – | |||
| 12q23.3 | CKAP4 | Cytoskeleton-associated protein 4 | X69910 | –2.45 | .029 | –2.47 | .028 | – | – | |||
| 13q12 | HMGB1 | High-mobility group box 1 | D63874 | – | – | –3.15 | .030 | – | – | |||
| 13q12.1 | SAP18 | Sin3-associated polypeptide, 18 kDa | U96915 | – | – | –4.41 | .042 | – | – | |||
| 13q12.3-q1 3.1 | GTF3A | General transcription factor IIIA | D32257 | –2.81 | .045 | –3.2 | .036 | – | – | |||
| 13q12-q13 | CG018 | Hypothetical gene CG018 | AL049786 | 1.74 | .011 | – | – | – | – | |||
| 13q12-q14 | TPT1 | Tumor protein, translationally controlled 1 | X16064 | – | – | –1.55 | <.001 | – | – | |||
| 13q14.11 | MRPS31 | Mitochondrial ribosomal protein S31 | Z68747 | – | – | –3.21 | .010 | – | – | |||
| 13q31.2-q3 2.3 | STK24 | Serine/threonine kinase 24 (STE20 homolog, yeast) | AF024636 | –3.31 | .004 | –4.57 | .004 | – | – | |||
| 13q32 | ZIC2 | Zic family member 2 (odd-paired homolog, Drosophila) | AF104902 | – | – | 1.31 | .008 | – | – | |||
| 13q32.3 | TM9SF2 | Transmembrane 9 superfamily member 2 | U81006 | –3.23 | .020 | –4.28 | .013 | – | – | |||
| 13q34 | ATP11A | ATPase, class VI, type 11A | AB028944 | 2.34 | .001 | 1.96 | .003 | – | – | |||
| 13q34 | LAMP1 | Lysosomal-associated membrane protein 1 | J04182 | –2.9 | .013 | –4.47 | .008 | – | – | |||
| 14q22-q24 | ZFP36L1 | Zinc finger protein 36, C3H type-like 1 | X79067 | –5.6 | .006 | –7.45 | .004 | – | – | |||
| 14q24.1 | ACTN1 | Actinin, α 1 | X15804 | – | – | – | – | –23.19 | .046 | |||
| 16q12.2-q13 | HERPUD1 | Endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 | D14695 | –1.99 | .013 | –2.94 | <.001 | – | – | |||
| 16q13 | CNGB1 | Cyclic nucleotide gated channel β 1 | U18945 | 2.92 | <.001 | 2.84 | .002 | – | – | |||
| 16q22.3q24.1 | GABARAPL2 | GABA(A) receptor-associated protein-like 2 | AI565760 | –2.44 | .042 | –2.92 | .027 | – | – | |||
| 16q22-q23 | MAF | v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) | AF055376 | – | – | –9.81 | .049 | – | – | |||
| 16q24.2 | MAP1LC3B | Microtubule-associated protein 1 light chain 3 β | W28807 | –2.12 | .031 | –3.53 | .008 | – | – | |||
| 16q24.3 | RPL13 | Ribosomal protein L13 | X64707 | – | – | – | – | 1.5 | .043 | |||
| 17p13.1 | GABARAP | GABA(A) receptor-associated protein | AF044671 | –2.52 | .031 | –3.26 | .020 | – | – | |||
| 17p13.1 | SENP3 | SUMO1/sentrin/SMT3 specific protease 3 | AL050283 | – | – | 2.04 | .041 | – | – | |||
| 17p13.1 | CD68 | Serine/threonine kinase 17b (apoptosis-inducing) | AA203487 | – | – | – | – | –2.02 | .009 | |||
| 20p12 | BMP2 | Bone morphogenetic protein 2 | M22489 | – | – | 85.74 | .002 | 10.71 | .039 | |||
| 20p12.1 | DSTN | Destrin (actin depolymerizing factor) | S65738 | – | – | –2.54 | .005 | – | – | |||
| 20p13 | SOX12 | SRY (sex determining region Y)-box 12 | U35612 | 1.62 | .017 | 1.98 | .004 | – | – | |||
| 20pter-p12 | PRNP | Prion protein | U29185 | –3.86 | .006 | –5.12 | .005 | – | – | |||
| 22q12.1 | TPST2 | Tyrosylprotein sulfotransferase 2 | AF049891 | –4.02 | .014 | –6.72 | .011 | – | – | |||
| 22q12.1 | XBP1 | X-box binding protein 1 | Z93930 | – | – | –1.72 | .002 | – | – | |||
| 22q13.1 | TOM1 | Target of myb1 (chicken) | AJ006973 | 3.07 | .009 | – | – | – | – | |||
| 22q13.31 | KIAA0153 | KIAA0153 protein | D63487 | – | – | 1.72 | .006 | – | – | |||
MM indicates multiple myeloma; –, gene not found in this comparison