CEI Molecular Diagnostics Laboratory
John (Pei-Wen) Chiang, PhD, FACMG, Director of CEI Molecular Diagnostics Laboratory
The Casey Eye Institute Molecular Diagnostics Laboratory is a CLIA certified laboratory providing comprehensive molecular testing for genetic diseases involving the eye. Our mission is to identify causative genetic mutation(s) in a timely and cost effective manner.
We would like to share our philosophy and service delivery model. In essence, client satisfaction is our core value and purpose.
To our valuable clients and families,
Casey Molecular Diagnostic Laboratory has exciting news to share with you. In our pursuit of developing the most comprehensive, specific and cost effective method for our NGS panels, we have combined the unmatched specificity of simplex PCR with the SmartChip platform from WaferGen. Simplex PCR reaction (100 nl per reaction) is run on a chip with 5,184 individual wells. An individual PCR primer set is printed into each well for the simplex PCR reaction. In order to avoid allele dropout and random PCR failure, each primer set is duplicated on the chip. This new development was made possible by the continuous effort to improve our PCR primer library. With this new platform, we now have the fastest, most consistent and simplest target enrichment method. Equally important, primers can now be managed easily because they are stored at room temperature inside the individually wrapped chip.
Our new approach offers unmatched on-target enrichment of sequencing targets (>98%). Our average coverage is >500X. Regions with coverage of less than 100X are further enriched by adding extra primers to the newer chip versions. Therefore, we do not need to rely on "sophisticated" variation filtering. Every novel variation, regardless of the scores, is checked manually in order to avoid false positive or false negative reporting.
While many laboratories in the molecular diagnostics field are trying to improve detection by sequencing more broadly, we still believe that "sequencing smart" is the best approach. Specificity, coverage and choice of targeted genes are all important to the improvement of mutation detection rate. By focusing only on genes relevant to the patient's condition, our testing approach has also been optimized to detect mutations in regions of genes frequently missed (such as introns and highly repetitive sequences) using methods such as whole exome sequencing. We aim to continuously improve our mutation detection rate by improving coverage and by adding newly discovered and relevant genes. Because we sequence smart, the (hidden) cost of data storage and the bioinformatics pipeline is significantly reduced. We believe our current approach offers the best value to our clients.
The family of SmartPanel:
Retinal Dystrophy panel v5 ($2,500): 211 genes; 4,180 simplex PCR duplicated on two chips (=8,360 simplex PCR). RD v6 is in manufacturing (227 genes plus LHON; 4,551 simplex PCR duplicated on two chips = 9,102 simplex PCR).
Stargardt/Macular dystrophy panel v3 ($500): 10 genes (each coding exon is covered by two primer designs; 511 simplex PCR duplicated on one chip (=1,022 simplex PCR; each coding exon is covered by four separate reactions).
Pigmentation panel v3 ($1,500): 29 genes (each coding exon is covered by two primer designs; 1506 simplex PCR duplicated on one chip (=3,012 simplex PCR; each coding exon is covered by four separate reactions).
Developmental eye disease panel v2 ($950): 45 genes; 606 simplex PCR duplicated on one chip (=1,212 simplex PCR).
Neurocutaneous panel v2: 8 genes; 672 simplex PCR duplicated on one chip (=1,344 simplex PCR).
Casey Geneticist and Collaborators Uncover Gene Linked to Severe Childhood Blindness
For nearly three years, Troy and Jennifer Stevens struggled to learn the identity of the gene responsible for their son Gavin’s blindness. Although doctors were able to diagnose him with Leber congenital amaurosis – a rare form of inherited childhood blindness – the first round of genetic testing could not pinpoint the defective gene.