For forensic DNA laboratories, data management and analysis are daunting tasks requiring numerous procedural steps and complex decision making. As a result, many laboratories rely heavily on their software systems to effectively manage their day-to-day laboratory operations.
Now you can streamline disjointed forensic data management workflows with Applied Biosystems Converge Software, a comprehensive forensic analysis platform that adapts to the way you work.
Converge Software offers streamlined solutions for next-generation sequencing (NGS) analysis of:
Designed to increase the efficiency of forensic and relationship DNA testing laboratories, the system is highly configurable to fit specific laboratory workflows, not only for analysis parameters, but also for incorporation of data fields according to your laboratory’s standard operating procedures (SOPs).
Designed to centralize all data management operations, such as analysis, reporting, and storage, Converge Software offers an all-inclusive, validated platform that elevates data processing efficiency. It’s also highly customizable to meet your lab’s needs, providing you with answers—integrated.
“ I have been waiting a long time for a software solution that integrates data management, analysis, and interpretation. Converge software, the newest tool for forensic genetic analyses, is a boon to our field.”
—Bruce Budowle, Institute of Applied Genetics, UNTHSC
Forensic scientists can now take advantage of Converge Software’s easy-to-use interface and highly flexible capabilities to optimize data creation, analysis, storage, and reporting.
Next-generation sequencing now makes it possible to sequence the mitochondrial genome (mtGenome), which increases discrimination and sensitivity. The Converge Software NGS Data Analysis module now gives forensic DNA laboratories the flexibility to detect variation within noncoding control region sequences or take full advantage of the genetic diversity with analysis of full mtGenome sequence data using either the Applied Biosystems Precision ID mtDNA Control Region Panel or Precision ID mtDNA Whole Genome Panel.
With an interface that is similar to that of Applied Biosystems GeneMapper ID-X Software, forensic analysts will be able to quickly evaluate NGS data of STR profiles, gaining information on STR allele call, STR sequence motif, known SNPs in flanking regions, and isometric heterozygote alleles of the same fragment length but containing different sequences.
Kinship and paternity analysis
Utilizing validated algorithms, Converge Software's Kinship and Paternity Analysis module offers laboratories the ability to conduct various types of relationship testing in a fraction of the time as compared to current methods. Users can quickly create a variety of hypotheses with easy-to-use pedigree tree–drawing capabilities and a set of comprehensive analysis parameters, including mutation model and population substructure.
In forensic casework, mitochondrial DNA (mtDNA) is useful in the context of challenging samples that fail to produce an autosomal STR profile due to their high copy number per cell. Traditional Sanger sequencing using capillary electrophoresis (CE) is generally limited to the sequencing of the hypervariable region. The Precision ID mtDNA Whole Genome Panel is an innovative approach to mitochondrial DNA sequencing specifically developed for forensic applications. This mtDNA tiling approach, using amplicons that are only 163 bp average length, assists with obtaining optimal mtGenome coverage from highly compromised, degraded samples such as hair shafts, teeth, and bones. The Precision ID mtDNA Control Region Panel is based on the same tiling approach used in the Precision ID mtDNA Whole Genome Panel. This targeted control region panel spans the entire 1.2-kb control region, which encompasses HV-I, HV-II, and HV-III, with the same optimal small amplicon design ideal for performance with degraded forensic samples. In addition, the panel design leverages primer degeneracy in known variable regions to ensure robust performance across diverse population samples. The Precision ID mtDNA Whole Genome Panel, using the control region data for analysis, is approved for inclusion in the US National DNA Index System (NDIS) CODIS database.
Analysis of the mtGenome can be challenging due to complex alignments, the presence mtDNA heteroplasmy, and insertions and deletions present throughout the genome that may impact the accuracy of variant calling. The automated mtDNA NGS analysis pipeline integrates various sources of knowledge for mtDNA variation, including PhyloTree and EMPOP, to provide fine-tuned alignments and variant calls that avoid the pitfalls of standard algorithms. Laboratories interested in more advanced analysis and reporting of mtDNA types can obtain haplotype and haplogroup information, along with quantitative assessments for point and length heteroplasmies, down to ~10% assuming a minimal sequencing coverage of >100x. NUMTs are insertions of mtDNA sequence into the nuclear genome and can be non-specifically (or non-intentionally) amplified with the mtDNA genome, presenting as a possible source of contamination. The Converge Software NGS Data Analysis module contains NUMT statistics and can detect and filter this type of contamination.
NGS reads are first mapped to nodes in PhyloTree and then realigned using a custom Smith–Waterman alignment algorithm that integrates PhyloTree and EMPOP information into the scoring function. Variants are called with reference to the rCRS. Additionally, the closest haplogroup is calculated, and variants are evaluated based on their occurrence in the haplogroup as well as other general metrics including frequency, strand bias, and coverage.
The Converge NGS Data Analysis module is required to generate profiles from the Applied Biosystems Precision ID GlobalFiler NGS STR Panel v2. The HID STR genotyper functionality provides discriminatory information on STR allele call, STR sequence motif, known SNPs in flanking regions, and isometric heterozygotes (alleles of the same fragment length but containing different sequences). These additional sources of allelic diversity may be useful in both mixture analysis and kinship interpretation.
With an interface that is similar to GeneMapper ID-X Software, forensic DNA analysts will be able to quickly evaluate data using familiar Process Quality Values (PQV) and flags such as allele number (AN), off-ladder allele (OL), peak height ratio (PHR), below stochastic threshold (BST) and control concordance (CC). Preconfigured analysis settings are provided within the NGS module and may be modified by the laboratory as needed. Additionally, full auditing functionality is included for chain of custody requirements.
Forensic samples may contain DNA that is too degraded to generate an STR profile—or there may be an STR profile that does not generate a potential match in a national DNA databank. These samples may be analyzed with SNP markers, either Ancestry Informative Markers (AIMs) to generate an investigative lead or identity markers to associate a degraded crime scene sample to a known reference. Converge Software NGS Data Analysis module contains analysis parameters for generating reports from the Precision ID Ancestry Panel and the Precision ID Identity Panel.
Converge SNP analysis provides a variety of metrics to monitor sequencing quality, including coverage of aligned reads to a hotspot, strand bias, number of reads containing each base at the hotspot, genotype call, and quality.
Tertiary ancestry analysis consists of generating an estimation of admixture prediction from seven geographical regions: Africa, America, East Asia, Europe, Oceania, South Asia, and Southwest Asia, and population likelihoods (based on algorithms from Ken Kidd).
Identity analysis consists of calculating Random Match Probability (RMP) based on genotype frequencies generated from 1000 Genomes data as well as a Y haplogroup prediction.
Underlying the centralization of data creation, analysis, and storage to one easy-to-access location, the Converge Case Management module supports case, subject, genotype profile, and laboratory data management.
The module serves the needs of various users such as laboratory managers and analysts, providing intuitive data views and reports that are configurable to the needs of each user and preserved for that user’s login. These features are easily accessible through a secured web browser under the protection of a laboratory’s IT department. The information management configurability allows the user to focus on pertinent information and adapts to a laboratory’s specific needs by enabling the addition of new data fields. Case data management includes metadata related to the case, subjects, DNA profiles, and attachments, with extensive data fields available to track all required information. Ideal for quickly reviewing case status and accessing case reports, the Case Dashboard functionality allows for an at-a-glance overview of the case. Extensive search and filtering capabilities on many data elements allow for faster access to relevant information, saving time and effort. Once performed, searches can be saved and viewed at a later date. Cases can also be exported for external sharing and storage and can be imported back as needed. Archiving cases can be scheduled or performed manually, allowing closed cases to be removed from the active dashboard. Should the need arise, archived cases can always be retrieved in the Case Dashboard.
The Case Details feature presents all case information in one view and allows access to case metadata such as case ID, requesting organization, description, priority, status, creation date, and owner. Added functionality allows the user to create and manage subjects through extensive subject details, capturing all necessary information that is saved, tracked, and retrieved. Subject details include, but are not limited to, name, date of birth, ethnicity, address, phone number, and government-issued identification. Additionally, exported DNA profi les from the NGS analysis module and GeneMapper ID-X Software can be imported and stored in Converge Software. The DNA profile along with its metadata, including the kit used to generate the data, is preserved. Multiple profiles utilizing different chemistry kits can be generated and associated with the same subject. Lastly, the attachments feature allows users to easily upload fi les like pictures, Microsoft™ Word™ documents, and Microsoft™ Excel™ fi les, organizing all case information in one location.
Kinship and paternity testing can provide challenges in both the sheer volume of cases to be analyzed, as well as the complexity of laboratory workflows and statistical analyses being performed. The Converge Kinship and Paternity module offers a comprehensive set of parameters to perform analysis, allowing laboratories to conduct various types of relationship testing in a fraction of the time as compared to current methods.
The Kinship and Paternity module incorporates STR data analyzed by GeneMapper ID-X Software from capillary electrophoresis–based multiplex panels such as the Applied Biosystems VeriFiler Express PCR Amplification Kit and GlobalFiler Express PCR Amplification Kit, from the Converge NGS analysis of the Applied Biosystems Precision ID GlobalFiler NGS STR Panel v2. Converge Software identifies and processes Trio Paternity, Trio Maternity, Duo Fatherless, and Duo Motherless kinship tests by automatically creating cases, adding subjects and profiles, running analyses, and generating reports. Users can quickly and easily create a variety of hypotheses by drawing pedigree trees and setting comprehensive analysis parameters, including application of mutation models and population substructures. It also allows for genetic likelihood ratio calculations, as well as the generation of custom reports for any complex relationship analysis. These analyses are conducted utilizing validated algorithms.
Through an intuitive user interface, analysts can easily review detailed results, as well as generate and electronically sign reports in a few simple steps. Converge Software provides one default report template; however, laboratories can use existing tools to modify this template and adjust the report to their desired format. For trio and duo testing in paternity and maternity cases, Quick Kinship Analysis (KA) functionality from the Case Dashboard integrates all of these steps on one screen, saving time within the laboratory.
Complex analysis parameters used in kinship analysis require validation in order to determine the appropriate settings for the thresholds governing the data interpretation. Therefore, it is important that the software be tested using a variety of samples that challenge each different relationship-testing scenario. Although default settings are suggested within the software, these should be adjusted based on the outcome of each laboratory’s internal evaluation of Converge Software. Optimizing any software will require an additional investment on the part of the laboratory. Extensive system verification has been performed at Thermo Fisher Scientific, and a summary of these verification studies are available as a reference guide for users interested in implementing the software.
Better data processing in a forensic laboratory starts with better software
Simplify the complexities of forensic DNA analysis with streamlined solutions for kinship and paternity analysis, NGS analysis and CE-NGS comparisons with Converge Software, a comprehensive enterprise software platform from Thermo Fisher Scientific. Designed to centralize all case data under one powerful solution, it’s an intuitive—and integrated—system for getting answers.
For Research Forensic or Paternity Use Only. Not for use in diagnostic procedures. For licensing and limited use restrictions visit thermofisher.com/HIDlicensing