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1,036,406 | 31476840 | 24,599 | 1036406 | Patient result; in the comparative genomic hybridization study conducted on the peripheral blood DNA, a duplication of 1114 kb (Hg19 coordinates: chr17:69006280-70120619) was detected in the region of 17q24.3. This duplication covers the region from 1.1 Mb upstream of the SOX9 gene (including the promoter region) to th... | [
146
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23
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0
] |
1,249,135 | 25476802 | 23,516 | 1249135 | The loss in chr3:181315609 to 181344028, which was found in both of the SFM-derived hUC-MSCs, did not appear in either of the SCM-expanded hUC-MSCs (Figure 3e). No annotated genes were located in this region, thus the CNV observed only in SFM-expanded hUC-MSCs might have little or no role in altering biological charact... | [
12
] | [
27
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0
] |
5,093,401 | 24720851 | 25,599 | 5093401 | A PCR assay with primers pointing outwards from the location of the first and last duplicated SNP in the Illumina Infinium 1 M-single SNP array confirmed that the duplication was in tandem and in the direct orientation (Figure 2). Sequencing of this PCR product defined the breakpoints of the duplication and determined ... | [
357
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22
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2,684,932 | 33443296 | 4,737 | 2684932 | Subject 1 (DECIPHER ID: 339928) was a Caucasian, 21-week gestation female fetus with left-sided CDH identified by prenatal ultrasound. The left lung was hypoplastic and the heart was displaced to the right. The stomach was in the thoracic cavity, but the remaining abdominal organs had normal conformations and positions... | [
744
] | [
21
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0
] |
3,988,722 | 24412158 | 21,005 | 3988722 | To determine whether the identified deletion interval [chr11:65690475-65695907 (hg18)] has previously been reported in the Database of Genomic Variants (DGV), the region was queried in the UCSC Genome Browser (http://genome.ucsc.edu/) using the 'DGV Structural Variation' track. We noticed that the 5.5kb deletion was se... | [
55
] | [
24
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0
] |
5,296,979 | 32795400 | 46,536 | 5296979 | Dual luciferase assay was performed using pGL4.23 (firefly, Promega #E8411) and pGL4.74 (Renilla, E6921) as transfection control. We cloned an 860bp region 5' of the Oct4 locus (positive control, Chr17:35504584-35505443) and 509 bp Lifr enhancer element (Chr15:7116691-7117199) using genomic DNA from 129S1 mice. To gene... | [
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1,918,938 | 32883984 | 35,724 | 1918938 | Gene ID Chromosome region (Galgal 5.0) Max ZFst value Min ZHp score Function related IGF-I Chr1:55,335,204-55,383,631 5.62 - 2.64 Body size SOX5 Chr1:65,938,356-66,226,982 9.90 - 5.20 Pea-comb APP Chr1:102,609,866-102,809,834 4.69 - 2.52 Autistic behavior and aggression AGMO Chr2:27,894,534-28,076,252 13.97 - 3... | [
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375,509 | 27114910 | 21,746 | 375509 | Gene name Locus Organism Uniprot ID Accession number PDB-ID CYP11A-cytochrome P450 side-chain cleavage enzyme (Marker Locus: D15S520) Chromosome 15: 74,367,990-74,368,179 Homo Sapiens P05108 P05108 3N9Y Sex hormone binding globulin Chromosome 17: 7,613,946-7,633,383 Homo Sapiens P04278 ABY68008 1D2S Luteinizing h... | [
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3,519,279 | 37988664 | 10,400 | 3519279 | The extracted DNA was segmented using DNA enzyme and purified by the magnetic bead method before being amplified by PCR and connected with the connector sequence. The target region of the whole exon group was captured and purified using the IDT xGen Exome Research panel probe, and the final library was sequenced on a N... | [
642
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24
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0
] |
4,464,637 | 37430472 | 10,154 | 4464637 | The patient was offered WGS as part of the STAGING study, a nation-wide WGS study offered to all patients newly diagnosed with pediatric cancer in Denmark from 2017 and onward (Byrjalsen et al., ). WGS revealed a germline 2.1 kb deletion including exon 14 of the SMARCA4 gene (NG_011556.3, GRCh38, chr19:11,007,277-11,00... | [
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3,994,243 | 21643010 | 29,416 | 3994243 | Primer walking was used to map the two breakpoints in Family 1, the primers can be obtained from the author upon request. The PCR primers used for the verification of the deletions were forward primer: 5'-CCAGGGAACTCAATCAAGGA-3' (chr5:111980705-111980724) and reverse primer: 5'-CTACCGCTTTGATCCCACAT-3' (chr5:112044642-1... | [
230
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4,840,571 | 39042694 | 23,160 | 4840571 | Because the LCR22AD deletion haplotype for patient 1728 contains the SD22-3 sequence (chr22:18518837-18622467) where it is directly proximal to the ~160 kb NAHR segment (Fig. 3D), we leveraged this SegDup configuration of the 1728 deletion haplotype to isolate only the 1728 NAHR region using CTLR-Seq for breakpoint ana... | [
86
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] |
1,043,046 | 27102850 | 40,798 | 1043046 | Gene name VCaP LNCaP DU145 PC3 Long ncRNA type ENST00000501280 62.0 21.4 21.4 14.7 bidirectional uc010bys.1 28.7 11.0 11.0 14.6 intergenic uc001qgn.1 50.0 5.4 5.4 3.0 intronic antisense ENST00000499690 15.4 16.2 16.2 8.5 intronic antisense ENST00000453968 48.5 2.5 2.5 2.3 intergenic G36642 46.0 3.0 3.0 2.2 ... | [
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1,617,599 | 29698419 | 39,216 | 1617599 | Evidence in support of ROBO1 as a susceptibility gene for a hereditary breast-colorectal cancer (HBCC) phenotype comes from a study by Villacis and colleagues. The aim of their study was to identify genomic alterations (copy number variations, CNVs) related to cancer predisposition in patients with a suggestive HBCC ph... | [
600
] | [
26
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] |
3,618,127 | 28611475 | 31,510 | 3618127 | C57BL/6 (WT) mice were purchased from the Australian BioResources. To generate Lrba-/- mice, an single-guide RNA with the sequence 5'-TTAACTGAGTTGCGGTCACATGG-3' (PAM underlined) was microinjected together with Cas9 mRNA into C57BL/6 zygotes. Four of the resulting founder mice were homozygous for an 8 bp deletion elimin... | [
326
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] |
3,662,746 | 27087860 | 18,526 | 3662746 | Fetus 11 (GA 28 + 3) was diagnosed by prenatal ultrasound with ACC (colpocephaly and absent septum pellucidum) and interhemispheric arachnoidal cysts. This fetus carried a 0.57-Mb deletion of chromosomal region 16p12.2 (chr16:21,839,340-22,409,463). This region comprises seven RefSeq genes namely UQCRC2 (ubiquinol-cyto... | [
220
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27
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921,662 | 40778130 | 51,051 | 921662 | (A) SR-WGS coverage in the duplication region (chr11:8,402,807-8,430,981) for subject REACH000426 confirms absence of the variant in both parents. The copy number increase in the proband does not reach a full additional copy, consistent with mosaic duplication. Coverage was computed in 500 bp windows. (B) Estimated cop... | [
47
] | [
25
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] |
2,230,498 | 25077177 | 22,411 | 2230498 | In order to confirm the microdeletion identified from the MLPA experiments, and to narrow the deletion breakpoints, we performed array-CGH experiments using a 1 million feature oligonucleotide microarray. A 19,971 bp deletion (chr5:50,676,490-50,696,460) was identified at chromosome 5q11.1 that affected 14 oligonucleot... | [
227
] | [
26
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339,532 | 31283647 | 18,423 | 339532 | In this study, we report a large Chinese family with severe generalized BD of hands and feet, pectus carinatum, and short stature. The BD feature of our patients presents with severe generalized BD, all metacarpals/metatarsals were shortened, and most phalanges were involved. The phenotypes of hands and feet in this fa... | [
777
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23
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1,843,642 | 30917130 | 19,205 | 1843642 | Using single-nucleotide polymorphism (SNP) microarrays, we analyzed a patient with global developmental delay harboring a 15q25 deletion and mapped the disease-critical region to a 1.6 Mbp region spanned by segmental duplication blocks A and B (Fig 4). To refine the breakpoints with greater precision, we performed whol... | [
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744
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1,330,372 | 30811755 | 9,642 | 1330372 | Read counts of deleted regions were calculated from BAM files and identified as belonging to 3 APOBEC3A/B classes (homozygous deletion, heterozygous deletion or wild-type) using k-means clustering. Germline CNV in the TCGA breast cancer database were also investigated by filtering using that same strategy as used for o... | [
557
] | [
28
] | [
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] |
582,638 | 30364518 | 5,346 | 582638 | The patient underwent genetic evaluation with a commercial arrhythmia panel involving 30 genes (GeneDx, Gaithersburg, MD; full list provided in Supplemental Appendix). No pathogenic variants were identified on direct DNA sequencing; however, targeted array analysis revealed a large deletion involving exons 4 to 14 of t... | [
362
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35
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3,954,223 | 33037779 | 15,543 | 3954223 | (A) MRI Brain at 10 months: Axial T2-weighted image shows mild T2 hyperintensity in the globi pallidi (arrowheads) and parietooccipital white matter (thin arrows). (B) MRI Brain at 29 months: Axial T2-weighted image shows abnormal T2 hyperintensity and decreased size of the bilateral thalami (block arrows), T2 hyperint... | [
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751,681 | 37745545 | 11,660 | 751681 | Other deletions that are in moderate LD (0.2 < R2 < 0.9) with GWAS signals can impact exons, enhancers, transposons, and conserved regions (Table 2). A 446 bp deletion (chr10:122457302-122457747) extending into exon 2 of ARMS2 is in LD (R2 = 0.24) with rs7908662 (chr10:122413396, PLEKHA1 intronic variant). A 310 bp del... | [
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3,246,876 | 36221102 | 5,245 | 3246876 | Direct Sanger sequencing of the 8 exons of PMM2 reported a seemingly homozygous variant rs200203569 NM_000303.3(PMM2): c.323C > T in exon 4. The variant leads to a missense substitution of alanine 108 to proline (p.Ala108Pro), commonly named A108V, known to be pathogenic (ClinVar, SIFT, Mutation Taster). The A108V muta... | [
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1,532,238 | 31333717 | 8,063 | 1532238 | Pedigree of the family and the characterization of the deletion breakpoints by gap-PCR. (A) Pedigree of this family. The arrow refers to the proband. The solid square (male) and circle (female) represent the two affected siblings; (B) Gap-PCR of family members using the peripheral blood-derived genomic DNA and primer s... | [
841
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4,510,702 | 33863876 | 7,134 | 4510702 | We obtained genomic DNA and lymphoblastoid cell lines from a female proband with acheiropodia and her parents. The proband has terminal transverse hemimelia of the four limbs with truncation of both hands and feet. Prior genetic testing identified a deletion overlapping exon 4 of the LMBR1 gene with an estimate for the... | [
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4,895,838 | 40009466 | 21,494 | 4895838 | Three downregulated circRNAs [chr19:9075304-9107468+, chr19:9048612-9077954+, and chr19:9108589-9166019+] and three upregulated circRNAs [chr19:9070732-9104755+, chr19:9069439-9161900+, and chr19:9067485-9102740+] were validated by qRT-PCR. The qRT-PCR expression level of both downregulated (Figure 9A) and upregulated ... | [
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1,227,379 | 32790717 | 10,845 | 1227379 | M5 function has not been investigated in transgenic preparations but its capacity to drive transcription in the oligodendrocyte CG-4 cell line was detected using transfected reporter constructs. Although the M5 enhancer displays only limited interspecies conservation, it is associated with a ChIP-Seq binding profile fo... | [
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1,126,538 | 25298407 | 34,880 | 1126538 | A-B' Representative microscopic images from hematoxylin and eosin-stained TRAMP sections from the prostate glands from which DNA was extracted for CGH analysis. A-A', TRAMP atypical hyperplasia of Tag (AHTag) at low (4x) and high-power (20x) respectively. B-B', TRAMP neuroendocrine carcinoma (NEC) at low (4x) and high-... | [
1696
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1,693,596 | 26561035 | 29,256 | 1693596 | Due to the high prevalence of CNVs in human genome, any potential pathogenic CNV needs to be shown to be absent in healthy individuals or patients with other unrelated diseases. We applied several filters to improve the confidences of our results. First, we collected a relatively large number of individuals who were he... | [
1070
] | [
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2,555,971 | 30971923 | 15,664 | 2555971 | In this study, two regions with relatively high levels of methylation in SAMP8, APP/PS1, and Control mice, were randomly chosen to validate the results of WGBS. Primers used to amplify AKT2 (Chromosome 1: 84411726-84450162+) and MAPK3 (Chromosome 1: 15412603-15613746+) are illustrated in Figure 5. Bisulfite conversion ... | [
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4,053,698 | 28697784 | 18,343 | 4053698 | It was not possible to characterize the deletion directly from WES because intergenic and intronic sequences are minimized. Sequence coverage indicated that the deletion was between SGCD exon 6 and TMD4. Furthermore, sporadic intronic and intergenic fragments were present 5' of exon 7, beginning at chr4:53282570, and i... | [
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3,648,949 | 28118382 | 15,258 | 3648949 | The syndromic presentation suggested the existence of a chromosomal alteration, which was investigated with aCGH (Fig 1). In the two siblings, there were 12 de novo CNVs (S2 Table): 8 in the female and 4 in the male. Filtering revealed that both siblings had 2 terminal chromosomal alterations: a 4.6-Mb duplication at 4... | [
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3,622,486 | 36440268 | 11,678 | 3622486 | Genes Sequences 1 chr11:74154652-74159524- Forward CATCTCCTACGCTTGCCTGA Reverse CCAGAGAAACAAAGTGGCACG 2 chr12:45412398-45412635- Forward GAGACGAACCCAACCTGGTG Reverse CGTGCCCTCCAAAATTGTACC 3 chr4:208359914-208362182+ Forward ACTGGTGTGAATACTCGGCG Reverse CTGTATGGGGCAATTCCGGT 4 chr7:137630261-1376489... | [
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1,632,532 | 31924697 | 10,079 | 1632532 | Last evaluation at 13 years of age revealed weight of 36.4 kg (8th percentile), height of 153.8 cm (32nd percentile) and head circumference of 54 cm (62nd percentile). Craniofacial features included a tall forehead and frontal bossing, high anterior hair line, hypertelorism with slightly down-slanting palpebral fissure... | [
731
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3,564,393 | 30921327 | 28,417 | 3564393 | HERV-Ks are the youngest family of endogenous retroviruses in humans and consequently they share considerable sequence identity. This has the effect of limiting the number of unique sites associated with some HERV-K, which decreases the size of the reference set T (S1 Dataset:virus). The set T is small for near identic... | [
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840,569 | 33863806 | 23,692 | 840569 | We detected a high VST signal in a CNV locus (Chr 1: 101,853,329-101,921,437) involving two adjoining genes involved in innate immune response, NLRP13 and NLRP8 (Fig. 4A). This association results from German Shepherds and Rottweilers having a different CN distribution than other breeds at this locus, probably due to t... | [
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914,268 | 19197363 | 56,507 | 914268 | Using comparative genomic hybridization, Kirov et al. reported 13 possible schizophrenia associated CNVs. One of these, a 1.4 Mb duplication including APBA2 and other genes was also found in our cohort and has already been discussed. The other CNV they designated as most likely to be pathogenic was a 250 kb deletion of... | [
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4,603,507 | 35240056 | 36,510 | 4603507 | (B) Effect sizes (beta; unit in the effect column) and p values (p) for the UKBB and EstBB GWAS, along with the number of individuals with available phenotypic data carrying a deletion, no CNV, or a duplication overlapping the CNV region. Labels indicate: (1) platelet count:1p36.11 (chr1: 25,599,041-25,648,747); (2) gl... | [
284
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3,306,078 | 24739123 | 5,821 | 3306078 | Clinical features of patient 2(A-E). Lateral (A, C) and frontal (B) view of the patient. The patient has facial asymmetry, sparse eyebrow, a large nasal tip and a long midface with a large mouth and crowding teeth. (D) Hands and (E) feet of the patient. Arrow indicates the surgically removed preaxial polydactyly. (F) H... | [
459
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2,849,359 | 41225980 | 30,013 | 2849359 | Array-CGH: the fetus presented a de novo terminal deletion of approximately 17.92 Mb, from 4p16.3 to 4p15.31 (genomic coordinates chr4: 37,336-17,953,610 [hg19]). | [
130
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792,242 | 40528303 | 49,361 | 792242 | Association of SVs with AD and enrichment analysis. (A) Association of SVs with AD. The red line represents an FDR of 0.05. The gray line represents an FDR of 0.2. One SV near RNA5SP293 and one SV on RABGAP1 with a FDR < 0.2 and replication p < 0.1 were marked red. (B) Controls carrying the duplication on RABGAP1 (chr9... | [
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5,038,096 | 36159974 | 86 | 5038096 | Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing and discovered four ra... | [
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1,493,644 | 41549095 | 11,292 | 1493644 | One of the objectives of this study was to characterise the functional consequences of the relatively understudied CYP2C19*37 allele, which is defined as a partial gene deletion that includes at least exon 1 (Fig. 3). The overall frequency of CYP2C19 deletions in EstBB was 1.9% based on genotyping array data (Supplemen... | [
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2,705,013 | 40564049 | 16,705 | 2705013 | Case #2: Of the 171,141 identified variants different from the reference genome, no P/LP germline point genetic variants were identified, including MET mutations. However, we detected an extended heterozygous duplication of 101,467 bp (chr7:116740252-116841718) in the patient, like in Case #1. In addition, a secondary ... | [
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1,817,575 | 30898144 | 22,588 | 1817575 | To study the contribution of TAD fusion to human diseases, we utilized a list of eight deletions that were validated to cause various disorders as a result of the genome structure disruption (Additional file 1: Table S1). We calculated the TAD fusion score of these eight deletions and compared against the TAD fusion sc... | [
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4,933,227 | 36168415 | 40,445 | 4933227 | circRNA miRNA(1) miRNA(2) miRNA(3) miRNA(4) miRNA(5) chr3:132050491-132051188+ hsa-miR-6829-5p hsa-miR-5006-5p hsa-miR-4446-3p hsa-miR-4753-3p hsa-miR-6859-5p chr18:51686135-51731527- hsa-miR-6739-3p hsa-miR-6874-3p hsa-miR-4679 hsa-miR-5182 hsa-miR-182-5p chr3:138289160-138291826- hsa-miR-4677-5p hsa-miR-6888-3p... | [
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2,920,899 | 40301690 | 21,610 | 2920899 | A 17-year-old male (Family 14, II.1) presented with a history of bilateral congenital cataract and high myopia, but no systemic anomalies. He had a family history of high myopia, but not congenital cataract. He carried a heterozygous de novo 1.9Mb 1q21 microdeletion involving GJA8 (Chr1:146020242-147909267 [hg38]) (Sup... | [
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3,144,341 | 33568206 | 20,402 | 3144341 | Diagnosed children Sample ID Group Sex Type CNV coordinates ASD/ID-associated CNV Reference coordinates Other information CNVs with a critical gene 1101366 ASD M Dup chr17:1,196,088-1,326,656 17p13.3 (Miller-Dieker syndrome) region (includes YWHAE and PAFAH1B1)^ chr17:1,247,833-2,588,909 Critical gene coordinates... | [
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1,287,117 | 27792995 | 41,172 | 1287117 | Per-allele log-odds ratios (ORs) were estimated using logistic regression, adjusted for principal components and study, as described previously. P-values were estimated using Wald test. For imputation, genotype data from 48,155 breast cancer cases and 43,612 controls were used to estimate genotypes for other common var... | [
366
] | [
29
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] |
3,261,711 | 27779662 | 9,468 | 3261711 | In the SNP array for Patient 1, a 10q terminal deletion with a breakpoint at 10q26.11 was detected (Fig. 1B). The deleted region was ~14.04 Mb in size (chr10: 121,385,398-135,427,143) and contained ~117 RefSeq genes (~83 known coding genes). In the SNP array for Patient 2, the 10q terminal deletion was ~13.04 Mb in siz... | [
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751,684 | 37745545 | 19,265 | 751684 | Since a significant homozygous CNV burden is detected, we performed association using a recessive model, of which assumes that two copies of the alternative allele are required to alter the risk. As a result, a 1 Kb deletion (chr11:131726334-131727274) in the intron of NTM is the only SV with FDR < 0.2 using the recess... | [
226
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4,259,613 | 34335682 | 17,491 | 4259613 | Chromosome n Size (Mb) NIPS Detected (n) CNVs Undetected (n) CNVs Location Size (Mb) Location Size (Mb) Chr1 4 1.3-4 2 del 1q21.1 4.0 2 dup 1q21.1q21.2 2.0 del 1q21.1 4.1 dup 1q21 1.3 Chr2 7 1.7-4.5 6 del 2q13 1.7 1 del 2p21p16.3 4.5 dup 2q13 2.0 del 2q13 1.7 dup 2q13 1.8 ... | [
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2,829,257 | 37563198 | 61,312 | 2829257 | Patient 3 (31606) is a 10-year-old female with a history of DD, speech delay, expressive language delays, and attention deficit hyperactivity disorder (ADHD). At 3 days old, she had chronic diarrhea and struggled with poor growth or weight gain. Over the course of her early life, she was hospitalized four times between... | [
1290
] | [
27
] | [
0
] |
4,360,614 | 27194416 | 2,640 | 4360614 | The cfDNA test used could detect aneuploidies across 22 autosomes and 16 chromosomal regions associated with 16 microdeletion diseases, including 22q11.21 (a region associated with 22q11.2 deletion syndrome; located at chr22:19,009,792-21,452,445 [hg19]). The cfDNA test results provided the first line of evidence for f... | [
219
] | [
28
] | [
0
] |
4,029,675 | 22028664 | 19,853 | 4029675 | The total number of A-to-G editing sites discovered by our screen is 15,646, of which 14,538 are unique. This the same order of magnitude as discovered in former editing screens. Almost all sites (13,668, 94%) are novel: they did not appear in DARNED, the most up to date database of RNA editing in humans. The 760 ultra... | [
20,
445
] | [
6,
25
] | [
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491,672 | 33157955 | 8,516 | 491672 | Affymetrix CytoScan HD array analysis including weighted log2 ratio, copy number state, mosaic copy number state, and allele difference for chromosome 1 showed an interstitial deletion at 1p33-p32.2. The genomic coordinates (hg19) are chr1: 47831383-58364913. The deleted region is denoted by a red bar. | [
235
] | [
23
] | [
0
] |
4,371,613 | 22022419 | 3,473 | 4371613 | Our initial examination of the genomic sequence between CFH and CFHR5 revealed duplicated segments, including several novel, highly similar, homologous regions (Figure S1, Text S1 and Table S1). In general, the high sequence identity among duplicated regions increases the probability of structural rearrangements due to... | [
1443,
1714
] | [
29,
28
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0,
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1,963,946 | 27840696 | 6,350 | 1963946 | In addition, aCGH of the proband also identified a 31.0-kb deletion of 4p16.2 (chr4:5,564,364-5,595,303; hg19) that included exons 17-22 of EVC2. This deletion was confirmed and subsequently detected in the healthy father by qPCR, suggesting that it is a paternally inherited loss-of-function allele for autosomal recess... | [
79
] | [
24
] | [
0
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2,772,218 | 38245557 | 17,649 | 2772218 | In total, 22 disease-associated SVs, 3 deep-intronic variants, and 2 non-canonical splice-site variants of IRD genes were found. Except for one inversion of ABHD12, SVs in the remaining 10 IRD genes were deletions (including homozygous, heterozygous, and hemizygous deletions), ranging from single exon to complete gene ... | [
781
] | [
18
] | [
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5,405,216 | 30732576 | 17,419 | 5405216 | Case # Sourcea Variant type Variant details Individual Sex Age group Inheritance Reported NDD phenotype(s) ASD DD/ID ADHD SCZ/psychosis Other 1 This report Multigene loss chr15:51,670,601-51,933,000 x 1262,400 bp (DMXL2, GLDN) Proband (II-1) F Adult Pat + - + - +b 2 Daughter (III-1) F Child Mat + +/- - - +b 3 ... | [
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186,732 | 34373684 | 11,096 | 186732 | Primers that flank the deletion breakpoints were designed for gap-PCR (A). Deletion of exons 12-24 was validated by Sanger sequencing. An 18,660-bp deletion covering exons 12-24 in PACS1 was identified (Chr11:65997403-66016062; hg19, GRCh37; B). Pedigree of individuals with exons 12-24 deletion in this three-generation... | [
203
] | [
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] | [
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4,019,827 | 27081517 | 11,834 | 4019827 | Gene Exon Genome position Variant AA subst. LOAD (n=960) EOAD (n=139) FTD (n=138) Controls (n=1456) (dbSNP139) Reference cases/controls MAF AD Pnominal Class PolyPhen2 (MAF) 1000G (MAF) ESP (cases/controls) Cruchaga et al. PLD3 Int 4 chr19:40872671 c.103-9T>A 1 Novel 0.00%/0.03% NS Nearsplice N/A N/F N/A N/A PL... | [
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3,131,044 | 31555424 | 5,677 | 3131044 | The DNA sample was sent to Sistemas Genomicos, Spain. The chromosomal microarray was completed using 4x180 CGH+SNP Microarray Kit (SurePrint G3 Human, Agilent Technologies). The array's results were analyzed with Agilent CytoGenomics v. 4.0.3.12 software, and the Aberration Detection Method 2 (ADM-2: 6.0) algorithm w... | [
464
] | [
26
] | [
0
] |
4,004,630 | 32656166 | 7,059 | 4004630 | Gene Genomic position (hg19) Mouse KO Phenotype* OMIM Disease association (inheritance) Genes that result in human monogenetic disorders that share features with VACTERL 1 AXIN1 chr16:337439-402676 VRL Caudal duplication anomaly (unknown) 2 B9D1 chr17:19240866-19281495 CRL Meckel syndrome (AR), Joubert syndrome ... | [
253
] | [
23
] | [
0
] |
1,326,272 | 34811950 | 18,622 | 1326272 | The fine tiling aCGH analysis combined with the breakpoint mapping revealed that the patient carried two distinct deletions: a smaller deletion of 719 bp (chrX:949,397-950,116, hg38) and a larger one of 235,154 bp (chrX:950,396-1,185,550, hg38) separated by 280 bp (Figure S1b), that were both inherited from the father ... | [
155,
215
] | [
20,
22
] | [
0,
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] |
1,714,924 | 20805873 | 5,592 | 1714924 | DMD 8772, a 22-year-old man, manifested severe muscle weakness, wheelchair dependency, and mild cardiac dysfunction. No evidence of dystrophin protein had been observed on a previous muscle biopsy, and the patient had been diagnosed with a frame-shift deletion of dystrophin exon 7 by multiplex ligation-dependent probe ... | [
999
] | [
33
] | [
0
] |
3,373,609 | 36370055 | 14,827 | 3373609 | For this study, the proband, her mother (III-1) and her father (III-2) karyotype analysis was normal (Figure 2a-c). Copy number variation sequencing showed a microdeletion at chromosome Xp in proband (IV-1). It was found that the proband inherited a deletion from her mother at nucleotide positions chrX:16996657-1739445... | [
299
] | [
22
] | [
0
] |
1,452,214 | 38628577 | 12,401 | 1452214 | Genetic investigations performed through CMA identified a 524,622bp loss at 12p11.22 (chr12:29,554,804-30,079,426) including the OVCH1-AS1, OVCH1, and TMTC1 genes, classified as a VUS (Figure 3B). There were no other CNVs in the genome. Identical CNVs found in the patient 2 were also observed in her older sister and he... | [
86
] | [
27
] | [
0
] |
1,903,580 | 35117655 | 13,959 | 1903580 | Gene Database Chromosome Variantclassification SIFT PolyPhen ARID1B CGC723 chr6:157099313-157099315:CAC:- In frame deletion NSR NSR BAZ1A CGC723 chr14:35234140-35234140:C:T Splice site NSR NSR BRCA2 CGC723_CPG114 chr13:32912123-32912123:G:A Missense Mutation Tolerated (0.87) Benign (0.011) CTNND1 CGC723 chr11:5... | [
149
] | [
23
] | [
0
] |
2,892,888 | 28003323 | 34,088 | 2892888 | Official symbol Also known as Genomic location Related disease Alteration Function CRNDE CRNDEP; PNAS-108; lincIRX5; LINC00180; NCRNA00180 16q12.2 UvealMelanoma Dysregulation CRNDE were associated with good prognosis via epigenetic mechanisms, particularly through histone methylation or demethylation by the PRC2 or C... | [
493,
2259,
2746
] | [
3,
9,
26
] | [
1,
3,
0
] |
1,116,031 | 35887306 | 36,823 | 1116031 | A further example of interesting hmsLRI-E overlapping microdeletions is represented by two intronic enhancers of ZEB2 (i.e., hmsLRI-E wTR1_3899, including wTR1_3900, Figure 6C), a gene whose mutations cause Mowat-Wilson Syndrome, characterized by intellectual disability and microcephaly and recently implicated in human... | [
422
] | [
24
] | [
0
] |
5,263,591 | 35187845 | 3,944 | 5263591 | Variant and inheritance Nucleotide changea Chr11:43859940G>C Chr11:43835725-43847793del Parent of origin Maternal Paternal Mutation type Missense Exonic deletion, frameshift cDNA mutationb c.610G>C c.392_501del Protein alteration p.A204P p.V131Dfs*51 Minor allele frequencyc 1KGP 0 N/A gnomAD 0 N/A ... | [
53,
65,
201,
242
] | [
11,
26,
6,
7
] | [
1,
0,
1,
2
] |
2,274,831 | 22686481 | 6,326 | 2274831 | NimbleGen whole-genome oligonucleotide aCGH profile for chromosome 2q. The ideogram (grey bars) depicts 2q22.1 to 2q22.3 genomic regions with the cytogenetic bands on the long arm of chromosome 2 (not on scale). The ~ 6 Mb interstitial deletion interval at 2q22.1-q22.3 [hg19, chr2: 138,750,000-144,750,000 bp] is indica... | [
277
] | [
32
] | [
0
] |
2,167,259 | 39910854 | 21,149 | 2167259 | After WES was performed, compound heterozygous variants were detected in the ABHD12 gene of the proband. M1 nonsense variant c.477G > A(p.Trp159Ter) resulted in the 159th codon changing from encoded tryptophan to terminating codon, this amino acid position exhibits high conservation across various species, thus produci... | [
125,
136,
1005,
1081
] | [
10,
11,
23,
23
] | [
1,
2,
1,
0
] |
1,695,244 | 28608987 | 14,482 | 1695244 | Ophthalmological anomalies have been reported in up to 62% of CSS patients, consisting of severe myopia (up to -18D) or, less often, strabismus, astigmatism, spherophakia, amblyopia, and optic disk coloboma 3. We observed congenital microphthalmia in the proband, a symptom that has never been reported before. Interesti... | [
537,
741,
769,
928
] | [
5,
11,
11,
27
] | [
2,
1,
2,
0
] |
413,329 | 31616639 | 12,981 | 413329 | atRNA gene name bGenomic coordinates and strand Tumor tissues Serum cCPM dFC dP-value dFDR (%) cCPM dFC dP-value dFDR (%) tRNA-Gly-CCC-1-2 chr1:16861920-16861991 + 39,401 2.1 <0.001 0.716 118,338 1.2 0.584 68 tRNA-Gly-CCC-chr1-137 chr1:16545938-16546009 - 12,631 2.1 0.001 3.875 37,450 1.1 0.705 79 tRNA-Gly-GC... | [
145,
239,
326,
416,
504,
595
] | [
24,
24,
25,
23,
25,
24
] | [
0,
0,
0,
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0
] |
5,401,038 | 26236399 | 7,355 | 5401038 | FISH analysis with XpYp subtelomere specific probes confirmed the microdeletion in the tip of chromosome X short arm (Fig. 2a) in all studied samples (III1, III3, III7, III10, IV2 and IV15). As the loss of PAR1 did not explain the neurologic phenotype observed in males, the DNA of carrier female IV2 was analysed by arr... | [
636
] | [
28
] | [
0
] |
1,791,555 | 21256485 | 20,743 | 1791555 | Microduplication locus (hg18) Patient Length (Mb) Genes within duplicated region chr 1: 119,652,659-119,966,935 POF-106 0.31 HAO2, HSD3B2, HSD3B1 chr 1: 119,719,096-119,953,605 POF-21 0.23 HAO2, HSD3B2, HSD3B1 chr 1: 237,422,778-237,602,136 POF-56 0.18 None chr 2: 51,536,418-51,865,782 POF-87 0.33 None chr 3:... | [
83
] | [
30
] | [
0
] |
3,953,208 | 30847195 | 4,011 | 3953208 | Graphical representation of the genes within the 9q31.2q32 microdeletion (chr9: 110,155,358-114,938,931, hg18). Generated using the University of California Santa Cruz genome browser GRCh36/hg18 (https://genome.uscs.edu) | [
74
] | [
29
] | [
0
] |
2,119,409 | 37386251 | 68,410 | 2119409 | (a) Schematic of the orthologous Fam5snv variant introduced into mouse. (b-e) Immunofluorescent staining for ISL1 (blue) and GATA2 (red) on cross sections from WT (b,c) and Fam5snv/snv (d,e) E14.5 hindbrains at r4 (b,d) and r6 (c,e) levels. Development of ISL1ON;GATA2ON IEEs was similar in WT (dashed region in b; inset... | [
631
] | [
28
] | [
0
] |
3,975,129 | 39815277 | 19,062 | 3975129 | Three structural variants were identified in G173-1 via OGM: a 52 kb inverted duplication ogm[GRCh38] dup(X)(p21.3p21.3) involving ChrX:28,471,891-28,523,939, a 604 kb CNV gain ogm[GRCh38] Xp22.31(8726692_9330458)x2 (ChrX:8726692-9330458), and an intrachromosomal fusion ogm[GRCh38] fus(X; X)(p22.31;p21.1) that was loca... | [
131,
217
] | [
26,
20
] | [
0,
0
] |
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