KGGSeq statistics
Tool stats & trends
Looking to identify usage trends or leading experts?

Protocols
KGGSeq specifications
Information
Unique identifier | OMICS_02260 |
---|---|
Name | KGGSeq |
Software type | Package/Module |
Interface | Graphical user interface |
Restrictions to use | None |
Operating system | Unix/Linux |
Computer skills | Medium |
Version | 0.8 |
Stability | Stable |
Maintained | Yes |
Taxon
-
Primates
- Homo sapiens
Subtool
- ISPP
Download

Versioning
No version available
Maintainer
- person_outline Miaoxin Li
Publications for KGGSeq
Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes.
A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases
KGGSeq citations
(26)CD70 Deficiency due to a Novel Mutation in a Patient with Severe Chronic EBV Infection Presenting As a Periodic Fever
[…] were processed using the GATK framework [version 2.8.1 ()], according to the GATK best practices recommendations (, ). Variants were classified as known or novel based on dbSNP146 and annotated using KGGSeq ().Annotations included positions in UCSC, RefGene, GENCODE and ENSEMBL transcripts, OMIM and ClinVar annotations, potential false positive signals, allele frequency in dbSNP, ESP6500, 1000 Gen […]
PDE1A polymorphism contributes to the susceptibility of nephrolithiasis
[…] on variants and estimated per-individual heterozygosity (~inbreeding), pairwise relatedness, and sex-check using PLINK (Additional file : Table S1). Variants quality control was conducted by software KGGSeq (http://statgenpro.psychiatry.hku.hk/limx/kggseq/ doc/UserManual.html), which were carefully designed to filter and prioritize gene variants in exome sequencing of rare Mendelian and common com […]
Rationale and design of GENEiUS: a prospective observational study on the genetic and environmental determinants of body mass index evolution in Canadian undergraduate students
[…] are. Gene-based association of SNPs with obesity trait level and change will be assessed using VEGAS2 software. Variant annotation and filtering from whole-exome sequences will be performed using the KGGSEQ framework. The association of well-established GWAS SNPs for BMI, WC, WHR and %BF, or a combination of pathogenic mutations in previously identified monogenic genes, with obesity trait level an […]
Dysfunction of Myosin Light‐Chain 4 (MYL4) Leads to Heritable Atrial Cardiomyopathy With Electrical, Contractile, and Structural Components: Evidence From Genetically‐Engineered Rats
[…] JA5, we performed exome sequencing in 2 patients, II‐1 and II‐3. In total, 62 960 single‐nucleotide variants and 4192 insertions/deletions (Indels) were detected after stringent quality control using KGGSeq (V0.8), and we chose the top 60 single‐nucleotide variants (listed in Table ) for validation according to their predicted pathogenic probability. It turned out that 2 missense single‐nucleotide […]
Exome Sequencing of Extended Families with Alzheimer’s Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function
[…] Alterations passing quality measurements were annotated with the KGGSeq and ANNOVAR programs [,]. Variants were normalized prior to annotation []. Ensembl, RefSeq, and Gencode transcripts were all annotated, and the top consequence per gene was used for prioritizat […]
Rapid Identification of Pathogenic Variants in Two Cases of Charcot Marie Tooth Disease by Gene Panel Sequencing
[…] within the exome regions included by wANNOVAR and those with allele frequency ≥0.05 in 1000 Genome project or ExAC database []. Pathogenicity prediction of nonsynonymous variants was performed using KGGSeq with default quality control criteria (--gty-qual 20 --gty-dp 4), additional option to predict Mendelian disease-causing and complex disease-causing variants (--mendel-causing-predict best --db […]
Citations
Looking to check out a full list of citations?

KGGSeq reviews
Be the first to review KGGSeq