Posted - December 2015 in Living with HSP - Management & Treatment News
And testing is getting cheaper
New techniques and technologies made possible by whole-exome sequencing (WES) and homozygosity mapping in a single step have significantly improved the ability to diagnose autosomal recessive disorders.
Homozygosity mapping is an effective approach for detecting molecular defects in consanguineous families by delineating stretches of genomic DNA that are identical by descent. Constant developments in next-generation sequencing created possibilities to combine whole-exome sequencing (WES) and homozygosity mapping in a single step.
Basic optimization of homozygosity mapping parameters was performed in a group of families with autosomal-recessive (AR) mutations for which both single-nucleotide polymorphism (SNP) array and WES data were available. We varied the criteria for SNP extraction and PLINK thresholds to estimate their effect on the accuracy of homozygosity mapping based on WES.
Our protocol showed high specificity and sensitivity for homozygosity detection and facilitated the identification of novel mutations in GAN, GBA2, and ZFYVE26 in four families affected by hereditary spastic paraplegia or Charcot-Marie-Tooth disease. Filtering and mapping with optimized parameters was integrated into the HOMWES (homozygosity mapping based on WES analysis) tool in the GenomeComb package for genomic data analysis.
We present recommendations for detection of homozygous regions based on WES data and a bioinformatics tool for their identification, which can be widely applied for studying AR disorders.
SOURCE: Genet Med. 2015 Oct 22. doi: 10.1038/gim.2015.139. [Epub ahead of print] PMID: 26492578 [PubMed – as supplied by publisher]
Novel mutations in genes causing hereditary spastic paraplegia and Charcot-Marie-Tooth neuropathy identified by an optimized protocol for homozygosity mapping based on whole-exome sequencing.
Kancheva D1,2,3, Atkinson D1,2, De Rijk P4, Zimon M1,2,5, Chamova T6, Mitev V3, Yaramis A7, Maria Fabrizi G8, Topaloglu H9, Tournev I6,10, Parma Y11, Battaloglu E12, Estrada-Cuzcano A1,2, Jordanova A1,2,3.
1Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.
2Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
3Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria.
4Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.
5Current address: Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
6Department of Neurology, Medical University-Sofia, Sofia, Bulgaria.
7Department of Pediatrics, Dicle University School of Medicine, Diyarbakir, Turkey.
8Department of Neurological, Neuropsychological, Morphological and Motor Sciences, University of Verona, Verona, Italy.
9Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
10Department of Cognitive Science and Psychology, New Bulgarian University, Sofia, Bulgaria.
11Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.
12Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey.
South African genetics pioneer offers cheap tests
Whole-exome sequencing for $250
A South African genetics testing service is offering health insured clients in South Africa and the UK whole-exome genetic testing for $250, more than 10 times cheaper than going rates currently.
A company formed by genome pioneer Craig Venter will offer clients of a South Africa-based insurance company whole exome sequencing – sequencing all protein-making genes in the human genome – at a price that marks yet another dramatic decline in the cost of gene sequencing
Venter’s company, Human Longevity Inc, will provide the tests at a cost of $250 each through a special incentive program offered by Discovery Ltd, an insurer with clients in South Africa and the United Kingdom.