Table 1.
Select loci enriched with CNVs in four major disease categories.
| Pheno | Cyto band | Del/ Dup | P-value | Gene name | Annotations |
|---|---|---|---|---|---|
| Cardio | 1p36.31 | del | 5.3E–14 | ACOT7, BACH, GPR153 | ACOT7 upregulation protects against fatty acid oversupply in the heart [21212523] |
| Neuro | 1q21.1 |
del dup |
6.0E–31 1.6E–27 |
BC036212, KIAA1693, NBPF1 | NBPF1 duplication in arteriovenous malformations [24098321] |
| Cancer | 2p24.3 | dup | 2.4E–61 | MYCN | Amplified/duplicated in neuroblastoma [23401364 and 15013217], DDX1-MYCN duplication in nephroblastoma [24161495] |
| Cancer | 2q31.1 | del | 6.2E–26 | GPR155, SCRN3 | Overexpressed in breast cancer [19022662], deletion in osteosarcoma [15298715], CNV reduced hepatocellular carcinoma cell line expression [28863781] |
| Aid | 4p13 | del | 1.7E–18 | SLC30A9, WDR21B | Zn regulation in white blood cells [25927708] |
| Cancer | 4p13 | del | 4.9E–23 | BEND4, CCDC4, SLC30A9 | BEND4 in colorectal cancer [21636702], CCDC4 in MDR pancreatic adenocarcinoma [18453221], deletion in bladder and other carcinomas [11906820] |
| Aid | 4p16.3 | dup | 1.4E–21 | RNF212 | E3 Ubiquitin ligase, involved in meiotic recombination [23396135] |
| Neuro | 4p16.3 | both | 2.5E–24 | TACC3, TMEM129 | Neurogenesis during cortical development [22842144], neuronal differentiation [20823227] |
| Neuro | 5q23.1 | dup | 3.8E–27 | TNFAIP8 | Induced in Parkinson’s disease [24444419] |
| Cancer | 5q31.2 | del | 3.5E–20 | HSPA9 | Medullary thyroid carcinoma [25435367], tumor suppressor signaling [23959801], oral SCC [23541579], HCC [17934217], colorectal cancer [15532096], brain tumors [9417864] |
| Neuro | 5q35.1 | del | 3.9E–23 | SLIT3 | Parkinson’s disease [19162339] |
| Neuro | 5q35.3 | dup | 6.6E–75 | GRK6 | Schizophrenia [21784156] |
| Neuro | 6p22.1 | dup | 1.8E–52 | HIST1H2AE, HIST1H2BG, HIST1H4E | HIST1H2BG associated with schizophrenia [23904455] |
| Cancer | 7p12.1 | dup | 5.1E–58 | DKFZP564N2472 | Lung adenocarcinoma [21151896] |
| Cancer | 7p12.2 | del | 3.7E–17 | IKZF1, ZNFN1A1 | Inactivation in lymphoma [11980663 and 11839096], deletion of IKZF1 or ZNFN1A1 in acute lymphoblastic leukemia [19129520, 26050650, 29519871, 15390181], |
| Aid | 7p15.3 | del | 6.9E–19 | ITGB8 | Inflammatory bowel disease [28067908] |
| Cancer | 8p22 | del | 7.5E–28 | SGCZ | Mutated in AML [24189654], recurrent copy number loss in breast cancer [29545918], downregulation of MiR-383 in intron of SGCZ [28243881], gene fusions NCAM2-SGCZ in metastatic small-cell gallbladder neuroendocrine carcinoma [28040546] |
| Cancer | 8q11.1 | dup | 2.0E–31 | AK097475, BC041354 | Upstream of CMYC, identified in prostate [16130124] and breast cancer [10867149, 15527903, 17213017] |
| Cancer | 8q24.13 | del | 1.6E–17 | TRIB1 | Leukemia [27390356], double minute in acute myeloid leukemia [18503831], colon cancer [19691111], prostate cancer [24962028] |
| Neuro | 10p14 | dup | 8.0E–19 | CUGBP2, NAPOR-1 | Neuroblastoma apoptosis-related RNA-binding protein [9858671] |
| Neuro | 10q22.2 | del | 1.5E–23 | ADK | Epilepsy and glioma [26329539] |
| Cancer | 10q26.3 | del | 8.4E–15 | TCERG1L | Silenced in colorectal cancer [22238052], higher methylation level in colorectal cancer [23546389, 22238052, 23321599] |
| Cancer | 11p12 | dup | 2.7E–26 | C11orf74, near CD44 | Marker for Langerhans cell sarcoma [25837753], disregulation of CD44 in different types of cancer [25025570, 30631039, 30443182, 30211160, 30317669, 30463359] |
| Aid | 11q13.4 | del | 1.8E–26 | UCP2 | Protective in sepsis [25873251], protective in inflammation [23925522], decrease the severity of multiple sclerosis in mice model [21857957] |
| Cancer | 11q22.3 | dup | 9.0E–18 | SLC35F2 | NSCLC [21874247], an important molecular determinant of response to the Sepantronium Bromide [25064833, 28465296, 25568070] |
| Neuro | 14q24.3 | dup | 5.9E–41 | C14orf43 | Pediatric pineal germinomas [27889662], vanishing white matter syndrome [22678813] |
| Aid | 14q31.3 | del | 4.5E–23 | FLRT2 | Autoantigen in SLE [23401699], prostate cancer [26890304] |
| Cancer | 16p13.3 | del | 4.4E–50 | MAPK8IP3 | Increased in brain tumor [16141199] |
| Neuro | 16p13.3 | del | 1.7E–18 | SOX8 | Neural crest development [16943273], loss of Sox8 alleles in Hirschsprung disease [15572147] |
| Neuro | 17q12 | del | 9.4E–18 | ACACA, C17orf78 | ACACA deleted in autism [23375656], ACACA associated with Alzheimer’s disease [22982105] |
| Neuro | 17q21.1 | dup | 5.7E–73 | NR1D1 | Major depression [23671070], bipolar disorder [26746321, 25359533] |
| Aid | 17q25.3 | dup | 6.1E–34 | SLC38A10 | Associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers [23382691] |
| Cancer | 19p13.3 | dup | 7.6E–25 | PALM | Cancer [28188128], CLL [28165464], lung cancer [25982285], near STK11, Peutz-Jehgers |
| Neuro | 19p13.3 | dup | 6.5E–47 | HCN2, POLRMT | Decreased HCN2 reduces learning abilities [21593326], HCN2 gene deletion decreased neuropathic pain [21903816] |
| Cardio | 22q11.21 | del | 3.7E–23 | COMT, TBX1 | Velocardiofacial syndrome [26278718] |
CNVRs presented in Table 1 show disease category-specific enrichment reaching statistical significance (P < 9 × 10−14), which is adjusted for multiple comparisons based on results obtained from repeated simulations (see Methods). See Supplementary Data 5 for extended results (P < 5 × 10−8). Brackets [notation] denote PMIDs