Predictive Laboratories, Inc., a Salt Lake City, UT biotechnology Company formed in 2017, is a molecular laboratory focusing on human infertility, women's health, and childhood diseases and performs genetic testing using state-of-the-art instrumentation. The clinical leadership team includes Laboratory Director Kenneth Ward, M.D. who is Board Certified in four specialties including Obstetrics and Gynecology, Maternal-Fetal Medicine, Medical Genetics, and Molecular Genetics. Dr. Ward has run DNA diagnostic laboratories for more than 32 years and is internationally known in the field of human genetics. Lesa Nelson serves as Chief Operations Officer and has more than 30 years of experience in Human Molecular Genetics. Justine Coppinger, M.S., a Board-Certified Genetic Counselor, serves as Director of Clinical Affairs and brings more than 20 years of experience in clinical and diagnostic laboratory settings. Predictive Laboratories voluntarily participates in proficiency testing programs and adheres to strict accreditation standards and practices of the College of American Pathologists (CAP), the Clinical Laboratory Improvement Amendments of ‘88 (CLIA), and all applicable state licensing.
Whole Exome Sequencing (WES) is designed to sequence all the protein-coding regions in a genome, collectively referred to as an exome. The exome represents less than 2% of the genome and is comprised of approximately 180,000 exons. Since 85% of all disease-causing sequence variants are located in protein-coding regions of the genome, WES is an efficient method for identifying the underlying causes of both common and rare diseases. Predictive Laboratories provides high quality WES services to achieve high exome coverage required for accurate and reliable variant discovery.
WES Service Details:
• Exome libraries are produced using the Ion Ampliseq Exome Library Kit.
• The Ampliseq Kit is designed to target ~33Mb of coding exons. Greater than 97% of coding regions as described by consensus coding sequences (cCDS) annotation are amplified in 12 primer pools, 294,000 primer pairs, for highly specific enrichment of exons within the human genome.
• The whole exome is then sequenced using the Ion Proton or Ion S5 sequencing platform with 200 bp amplicon read technology using a P1V3 chip.
• Following data collection, the exome DNA sequences generated for each sample are aligned and compared to human genome build UCSC hg19 reference sequence using the Ion Torrent Suite software v4.2.
• Deliverables include FASTQ, VCF, BAM, and BAI files as desired. Additional bioinformatic analyses is available upon request; please contact us for pricing.
• Mean depth coverage ranges from 30x up to > 100x depending on customers requirements.
• Predictive's WES services are provided as Research Use Only (RUO), but all work is conducted in a CAP/CLIA environment.
The Ion Torrent platform allows for sequence analysis for targeted gene panels in situations where whole genome or whole exome analysis is not required. This platform allows for the creation of customized panels that can be tailored to specific DNA segments, genes or alleles to meet your sequencing requirements.
• If not specifically provided by the customer Predictive will perform bioinformatics analysis to determine the total number of amplicons required to ensure complete coverage of the SNPs, genes or alleles targeted by the customer.
• All amplicons are simultaneous amplified in a single large pool using primer pairs customized to the customers targeted sequences.
• Library preparation for sequencing is performed using the Ion AmpliSeq Kit for Chef DL8 library kit. Each sample is labeled with a unique DNA barcode and the Ion Chef System is utilized to automate workflow and chip loading prior to sequencing.
• Sequencing is conducted on the Ion Proton or Ion S5 instrument using the Ion P1 Chip Kit 2x150bp chemistry.
• Data is reported in a secure electronic format in the form of FastQ, VCF or BAM files.
• Data Interpretation & Analysis is available upon request; fees are dependent on the scope of the project.
Predictive Laboratories offers both manual and automated DNA Extraction services for the following sample types:
• Buccal swab
• Buffy Coat (WBC)
• Body Fluids
High throughput automated DNA extraction performed using the Chemagic MSM I 96-well Automated DNA Extraction Workstations (Perkin Elmer). Sample preparation is based on M-PVA Magnetic Bead technology.
Our laboratory is well-equipped to determine quantity and quality of extracted DNA:
• NanoDrop ND-1000 Spectrophotometer
• PicoGreen analysis with the BioTek Synergy-2 Fluorometer
• Agarose Gel Electrophoresis using UVP Gel Documentation System
• Bio-Rad Molecular Imager Gel Doc XR System
Sample integrity is maintained during sample preparation and storage by creating labels with the Zebra ZM400 Thermal Printers.
NGS SEQUENCING LIBRARY PREP
• Genome / Exome
• AmpliSeq 2.0 (custom Primer sets/panels)
• Ion Xpress Fragment (De novo)
• Exome (human sample, batch processing)
• Genome (non-human, plant/fungi)
• Genome Prime (3-4 fungi samples)
• Ion Torrent Proton Next Generation Sequencing Systems
• Ion Torrent Chef Support Systems
• Ion Torrent S5
Data delivery options include raw FastQ, VCF, BAM and BAI files. All data is transferred using secured methods.
Predictive Laboratories offers a broad range of Single Nucleotide Polymorphism (SNP) genotyping services that are customizable to meet your needs (research, clinical, direct-to-consumer) for any large or small-scale project. SNP Genotyping Service Description: • SNP discovery, primer design, validation and screening available if required. • SNP detection is based on the TaqMan SNP Genotyping Assays from Applied Biosystems. • SNP sequence detection also available with the QuantStudio 5 Real-Time PCR System from Applied Biosystems in either 96 or 384-well format. • Single tube and/or multiplex SNP genotyping available • OpenArray Real-Time PCR with QuantStudio 12k Flex provides flexible SNP genotyping capabilities for optimization of the number of samples to be tested vs the number of SNPs required. This system utilizes the robust TaqMan chemistry platform and can be customized to match your requirements. • All data is reported in user friendly formats with flexible reporting options including fluorescent scans and/or genotypes in spreadsheet format.
Predictive Laboratories offers the following genotyping services:
Sequence variation detection:
• OpenArray Real-Time PCR with QuantStudio 12k Flex or QuantStudio 5
• Ion Torrent targeted Next Generation Sequencing (NGS)
• Thermo Fisher GeneTitan MC system
Fragment analysis detection:
• Thermo Fisher Applied Biosystems 3500 or 3130xl Series Genetic Analyzer System
Predictive Laboratories experienced Bioinformatics team utilizes advanced methodologies to produce accurate, high quality and reproducible results. We provide streamlined bioinformatics solutions including experimental design, expert consultation, technical and scientific support. Our Bioinformatics solutions are available as a standalone service or as a component to our Next Generation Sequencing (NGS) services. Reports are delivered in a secure format and deliverables include Quality Control Summary Report, Data Analysis Report and raw sequencing and alignment data.
Chromosomal microarray analysis is a method of measuring gains and losses of DNA throughout the human genome. It is a high-resolution whole-genome screening that can identify major chromosomal aneuploidy as well as the location and type of specific genetic changes that are too small to be detected by conventional karyotyping.
The most common reasons for performing cytogenetic studies for prenatal diagnosis include advanced maternal age, abnormal prenatal screen, a previous child with a chromosome abnormality, abnormal fetal ultrasound, or a family history of a chromosome abnormality. Chromosomal microarray (CMA) is a high-resolution method for detecting copy number changes (gains or losses) across the entire genome in a single assay and is sometimes called a molecular karyotype. The American College of Obstetricians and Gynecologists and the Society for Maternal-Fetal Medicine recommend the chromosomal microarray as a replacement for the fetal karyotype in patients with a pregnancy demonstrating 1 or more major structural abnormalities on ultrasound when undergoing invasive prenatal diagnosis.
This CMA test utilizes >1.9 million copy number probes and approximately 750,000 single nucleotide polymorphism (SNP) probes for the detection of copy number changes and regions with absence of heterozygosity (AOH).
Predictive Laboratories is well-equipped to run chromosome microarray and utilizes the Affymetrix™ GeneChip™ Scanner 3000 systems, including hybridization ovens, automated fluidics stations and high-resolution scanners. Predictive Laboratories is also equipped to run the GeneTitan multi-channel instrument.
Predictive Laboratories specializes in TaqMan testing services including real-time quantitative polymerase chain reaction (qPCR) and SNP genotyping. We utilize the Applied BioSystems Quant Studio 5 Real Time PCR System which allows for either 96- and 384-well formats to accommodate high-throughput projects. Predictive also utilizes the Applied BioSystems OpenArray Genotyping Instruments (QuantStudio 12K Flex Real Time PCR System) including the AccuFill™ Sample Loading System. Users may also choose to submit their own genes and/or primer pairs or work with Predictive Laboratories for assay design services; please contact us for assay design information and pricing.
Assays (16, 32, 64, 128, 256 array format)
Predictive Laboratories offers fragment analysis services using either our Applied BioSystems 3730 XL for large sample projects or the ABI 3130 XL DNA Analyzer for smaller projects.
Fragment Analysis Applications Include:
• Microsatellite Analysis
o Parentage verification and identity/relationship testing
• VNTR Genotyping
• Mutation Detection
• Fragile X (CGG repeats)
• SMA Carrier Testing
Predictive Laboratories offers RNA extraction and quality control for a variety of sample types including:
• Whole Blood
• Buffy Coat
• FFPE Tissue
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