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Protocols

LSDBs specifications

Information


Unique identifier OMICS_00274
Name LSDBs
Alternative name Locus-Specific DataBases
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

LSDBs citations

 (11)
call_split

Diagnosis of lethal or prenatal‐onset autosomal recessive disorders by parental exome sequencing

2017
Prenat Diagn
PMCID: 5836855
PMID: 29096039
DOI: 10.1002/pd.5175
call_split See protocol

[…] ntified for further investigation by comparison with the fetal phenotype. Previous reports of a variant were determined by using HGMD professional, ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) and Locus‐specific databases. In silico tools were accessed via Alamut Visual (versions 2.7.2‐2.10) to predict pathogenicity of variants. Likely causative variants identified in this series were variants […]

library_books

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges

2017
Comput Struct Biotechnol J
PMCID: 5581845
PMID: 28883909
DOI: 10.1016/j.csbj.2017.07.004

[…] are the first works to report the performance at 62 GCUPS and 70 GCUPS, respectively. The original XSW implementation is based on native model, which limited the database size. In the follow up work LSDBS  proposed in 2015, the limitation on database size is removed, and the CPUs are also involved in the computing pipeline. LSDBD uses a dynamic distribution strategy to balance the workload among […]

library_books

Novel BRCA1 and BRCA2 Tumor Test as Basis for Treatment Decisions and Referral for Genetic Counselling of Patients with Ovarian Carcinomas

2016
Hum Mutat
PMCID: 5248611
PMID: 27767231
DOI: 10.1002/humu.23137

[…] Remaining variants were validated using Sanger sequencing or by independent resequencing of the corresponding sample using our smMIP‐based targeted sequencing approach. Variants were submitted to the locus‐specific databases at LOVD: www.lovd.nl/BRCA1, www.lovd.nl/BRCA2.To determine the accuracy per nucleotide of our method, we determined the number of true positives (n = 996), false positives (n […]

library_books

Paclitaxel is necessary for improved survival in epithelial ovarian cancers with homologous recombination gene mutations

2016
Oncotarget
PMCID: 5217039
PMID: 27191893
DOI: 10.18632/oncotarget.9373

[…] was achieved in less than 50% of targets. Variant identification and classification was performed using a strict filtering and analysis pipeline that has previously been described and validated [, ]. Locus-specific databases, ClinVar, dbSNP, and COSMIC were utilized to help identify suspected deleterious variants, and any missense variant calls that could not be confirmed in the literature were co […]

call_split

Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next generation cancer panel testing

2015
Genet Med
PMCID: 4985612
PMID: 26681312
DOI: 10.1038/gim.2015.166
call_split See protocol

[…] eticists. Specific tools and resources include the Exome Sequencing Project, SIFT, PolyPhen2, MutationTaster, splice site prediction model BDGP, NetGene2, Softberry, Human Gene Mutation Database, and locus-specific databases including the Breast Cancer Information Core and InSiGHT.Evidence supporting benign classification of a variant included, but was not limited to, silent variants without evide […]

library_books

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

2012
BMC Genomics
PMCID: 3303716
PMID: 22759650
DOI: 10.1186/1471-2164-13-S4-S2

[…] requested to submit their datasets to VariBench to be distributed to the community.VariBench datasets have been collected from literature as well as with data mining approaches from diverse sources. Locus specific databases (LSDBs) are the most reliable source for disease-related data. Although lots of variation data are listed in LSDBs, it would be necessary to capture to databases all the cases […]


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