Registered nurse (operating room) for over 27 years, "semi-retired". PGP participant, tested by at least a dozen retail and/or non-profit genomics testing companies/institutions over the past ten years, and 12 members of my immediate family (spanning four generations) tested by various retail genomics testing companies, & whole exomes (x2) for immediate family. Great interest in archaeology (particularly, forensic genomics) and human origins, but primary interests shifting to molecular genetics.
Sporadic ALS,LOAD (APOE-e2/e3), sporadic Parkinson’s Disease and Idiopathic Generalized Epilepsy in immediate and extended family, no causal variants identified to date, May 2019. Our family is very open to working with researchers attempting to decipher these devastating disorders. sALS trio, comprised of PGP whole genome (VCF only), and two whole exomes as noted below. Please contact me directly (email@example.com) if you wish to use whole exome data files for additional family members. (Platform: Illumina HiSeq; Enrichment: Nextera Rapid Capture Expanded Exome Kit - FC-140-1006, Average 70X Coverage, BAM, FASTQ and VCF files available). Five autosomal recessive variants (heterozygous only) identified to date, including HEXA (R170W) We are currently focused on searching for clinically significant de novo mutations and autosomal recessive compound heterozygous variants.
I have lately become increasingly aware of the need to use a variety of technologies to get an accurate genome assessment, e.g, Next Generation Sequencing, Long Read Sequencing (Pac-Bio), genotyping, Sanger Sequencing (for confirmation of variants), HLA imputation from NGS & Pac-Bio, NanoPore MINION long read sequencing, virtual karyotyping, etc., and I continue to explore any affordable avenues to access those technologies. May 2019 update - BioNano Genomics relatively new Saphyr structural variant analysis is of great interest at present. This technology appears to be emergin as a leading contender for structural variant analyisis, and I am actively engaged in searching this sequencing service from any lab that has access to the technology.
Update May 2022 - My son Sean chose a medically assisted death seven years after diagnosis with sporadic ALS and after more than 18 months on a ventilator. He died August 6, 2019 and six months later the pandemic emerged. It seems readily apparent now that “most” sporadic ALS is of epigenetic origin. I would surmise that many other sporadic neurodegenerative diseases (e.g. sporadic Parkinson’s and sporadic LOAD) are also of epigenetic origin, the result of genome dysregulation secondary to environmental/developmental “triggers”,, and accumulation of histone modification markers. It is increasingly apparent that the new hybrid technology de novo whole genome sequencing is clearly a necessity for deciphering complex neurodegenerative diseases when Mendelian disease has been ruled out.. Since population scale hybrid technology de novo assembly represents an astronomical investment of resources, I don’t see much hope for a true diagnostic whole genome in the near future. The only hope is a near miraculous reduction in cost for long read sequencing with optical mapping, etc.Hoping for the next genius(s) to get us there, Existing technologies obviously represent a huge leap for medicine since the beginning of the 21st century, but there is still a long road ahead before it becomes available for mass consumption, all while the specter of global war and catastrophic climate change is crouched to spring upon us. Carpe diem.
American Gut Project
Harvard Personal Genome Project