QIAGEN® Human ID and Forensics

Massively Parallel
Sequencing Solutions for
Human Identity

Sample to Insight
 Sometimes
an investigation goes cold

Human identity testing has been a force for good since Single Nucleotide Polymorphisms: the next paradigm in
its inception over three decades ago. HID techniques can human identity
be applied to identifying a criminal suspect, confirming Single nucleotide polymorphisms (SNPs) have the potential
someone’s innocence, or repatriating a missing person’s to address these challenges in the current human identity
remains to their grieving family. However, although forensic workflow. Amplified fragments used to genotype SNPs can
science has advanced steadily, established methods have be very short, making SNPs potentially more successful
their limits, and sometimes an investigation goes cold. than STRs when the DNA is extremely degraded. Such
DNA recovered from crime scenes, mass and natural small amplicons are also much easier to multiplex in large
disasters and other human ID scenarios are frequently numbers offering higher levels of discrimination. SNPs
degraded through exposure and over time. In addition, in closely linked sets can be jointly genotyped by MPS
successful analysis with current methods is frequently (Massively Parallel Sequencing) techniques. These phased
hindered by the error-prone PCR assay, which introduces microhaplotypes have multiple alleles, thereby increasing
artifacts such as ‘stutter’ which complicate interpretation. As their discriminating power. When combined with large SNP
a result, confidence in results is sometimes low. Furthermore, multiplexes, these microhaplotypes enable discrimination
even when the current methods work correctly, a criminal power unrivaled by STRs. SNPs also offer less opportunity
investigation may stall if there is no suspect to compare to a for enzyme slippage during PCR making interpretation
crime scene sample; there is no way to use the DNA result. easier.

Current methods are often not sufficiently discriminating, Many forensic genetics experts foresee that an SNP-based
particularly in cases involving familial testing, e.g., when approach may best capitalize on the strengths of NGS.
addressing complicated paternity questions or identifying
victims from mass graves.

2  Massively Parallel Sequencing Solutions for Human Identity 09/2020

Next-generation sequencing using QIAGEN’s
QIAseq® – a powerful tool for human identification

HumanIDIDsolutions
Human solutionsforfor
thethe MiSeq
MiSeq® and
and S5 S5

Sample DNA Target Library

Sequencing Analysis
Collection Purification Amplification Preparation

SNPs

Collectors and QIAamp QIAseq Targeted DNA panels: Compatible with Genomics
Collection Kits Investigator Kit QIAseq targeted DNA custom panels the S5 and MiSeq Workbench
Client/Server
Indicating EZ1 DNA Platform
FTA Cards Investigator Kit Mitochondrial DNA Custom
Bioinformatics
QIAsymphony QIAseq Human Mitochondria Panel Services and
Investigator Kit Solutions

Massively Parallel Sequencing Solutions for Human Identity 09/2020  3

 QIAseq
Targeted DNA Panels
Target the markers you need to inform your investigations

Accurate Robust
Avoid mistakes in interpretation due to stochastic PCR effects Optimized buffers, conditions and primer design deliver
thanks to our Unique Molecular Indices (UMI) technology. balanced results from your sequencing reactions, even for
UMIs are short sequences or molecular “tags” added to GC-rich regions, enabling easier downstream analysis and
DNA fragments in the library preparation protocol to iden- interpretation.
tify the input DNA molecule. UMIs are added before PCR
Platform agnostic
amplification and every molecule undergoing the first round
Each panel is a one-box, NGS platform-agnostic solution
of PCR is tagged independently. All copies of the same
that contains all the necessary components to amplify
target bear the same tag thereby assuring a significantly
your required targets and construct libraries ready for
higher confidence in the final sequencing data.
sequencing.
Discriminating
QIAseq panels confer unparalleled levels of discrimination Flexible

with highly multiplexed SNP-based DNA markers that are In addition to offering separate QIAseq Investigator® panels

more informative than previous methods (STR). Complex for a wide range of HID applications, custom panels can

family relationships can be confirmed where previously such be designed easily and quickly to target your regions of

questions remained unanswered. interest. This enables you to design your own panel to meet
your own specific research or casework needs. Panels can
Sensitive
be built and delivered within a few weeks. Using the robust
QIAseq panels allow unrivaled confidence in your results,
QIAseq chemistry gives you high confidence that your panel
even with highly degraded, trace samples, meaning more
will work straight out of the box without further optimization.
casework samples are viable for testing than ever before.

Intelligent
QIAseq panels also offer valuable information to further
human ID forensic investigations when there are no suspects,
such as trait prediction and ancestry information.
The power of massively parallel sequencing for human
identity testing is finally realized with QIAGEN’s QIAseq.

Visit GeneGlobe to discover the opportunities available to you to customize and optimize
your workflow. https://geneglobe.qiagen.com/product-groups/qiaseq-targeted-dna-panels

4  Massively Parallel Sequencing Solutions for Human Identity 09/2020

QIAseq Investigator
Missing Persons SNP panel
Developed in partnership with the International Commission
on Missing Persons (ICMP), the QIAseq Investigator Missing
Persons SNP panel includes more than 1200 tri-allelic
kinship SNPs in addition to 34 X-chromosome SNPs and
55 ancestry informative SNPs. Furthermore, the panel
includes a set of 46 microhaplotypes, and these combine
Catalogue number:
with the kinship SNPs to provide an unparalleled level of
CDHS-15861Z-2897, 333525
discrimination.
Number of primers:

2897
QIAseq Investigator ID SNP panel

Developed with leading paternity scientists, the QIAseq

Investigator ID SNP panel is designed to provide additional
discrimination where STRs fall short, either because of DNA
quality or the complexity of the analyzed (e.g., complex
pedigree/paternity/immigration cases).

Catalogue number:
CDHS-14055Z-277, 333525

Number of primers:

277
Mean coverage
100000

10000
Figure 1.
1000
Uniformity of coverage, for the 49 blood
samples, for the 139 SNPs in the target
100
enrichment panel sequenced on Illumina
MiSeq. All 139 SNPs are shown along the 10
x-axis and a logarithmic scale of coverage
on the y-axis. Only 1 SNP was below 1000X 1
coverage (the coverage of this SNP was
enough to make accurate calls. Marker

Massively Parallel Sequencing Solutions for Human Identity 09/2020  5

 QIAseq Investigator
Ancestry SNP panel

Based on the SNPforID consortium’s exhaustive

characterization of ancestry-informative
markers, the QIAseq Investigator Ancestry SNP
panel comprises subsets of markers aimed at
Global ancestry informative Middle East supplementary
accurately defining the key global population
marker set: marker set:
groups (Oceanian, American, African,
Catalogue number: Catalogue number: European, East Asian).
CDHS-12534Z-204, 333525 CDHS-12533Z-169, 333525

Number of primers: Number of primers:

204 169
Figure 2.
Sequence data from
the Investigator QIAseq
Ancestry SNP panel
can be further analyzed
using online tools such
as GenoGeographer [1].
Image reproduced with
kind permission of the
authors.

QIAseq Investigator
Microhaplotype panel
Ideally suited for applications in casework and
human identity such as mixture interpretation
and kinship testing, the QIAseq Investigator
Microhaplotype panel provides a comparable
level of discrimination to typical STR kits. These
markers can be further applied to missing
Catalogue number: person identification and paternity testing.
Inquire

Footnote
1. Tvedebrinka, T., Eriksen, P.S., Mogensen, H.S. and Morling, N. (2017) GenoGeographer – A tool for genogeographic inference. Forensic Sci. Int.:
Genet. 6, e463. https://doi.org/10.1016/j.fsigss.2017.09.196

6 Massively Parallel Sequencing Solutions for Human Identity 09/2020

Mitochondrial markers
Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of
recombination, a high copy number and matrilineal inheritance. Typing of mtDNA based on sequences of the control region
or full genomic sequences is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as
other biological samples where the DNA content is low. These panels give laboratories performing mtDNA casework the
flexibility to detect variation within noncoding control region sequences or exploit the genetic diversity by analyzing full
mtGenome sequence.

QIAseq Human Mitochondria panel

Ideally suited for challenging or degraded
remains, the QIAseq Human Mitochondria
panel enables sequencing of the whole
mitochondrial genome for casework, missing
persons and all applications in human
identification.

Whole mitochondrial genome Mitochondrial control region

marker set: marker set:
Catalogue numbers: Catalogue number:
DHS-105Z, 333502 or 333505 CDHS-13743Z-27, 333525

Number of primers: Number of primers:

Figure 3.
222 27
QIAGEN’s QIAseq mitochondrial DNA panels can be
analyzed with ease using the AQME mitochondrial DNA
plug-in tool for the CLC Genomics Workbench. Analysis is
Mitochondrial Control Region
straightforward and summary reports can be customized to
meet your needs. Left Primer 15,971 0 Control Region
1,210 bp

QIAseq Investigator 16,411

Right Primer
Human Mitochondria Control
Region panel
Human
In cases where only the control region sequence
Mitochondrial
is required, the QIAseq Investigator Human Genome
(16,569 bp)
Mitochondria Control Region panel enables
a simpler and easier alternative to whole
mitochondrial DNA sequencing.

Massively Parallel Sequencing Solutions for Human Identity 09/2020  7

 CLC Genomics Workbench
For analyzing, comparing and visualizing SNPs, mito-
chondrial DNA and other NGS data for human identity

CLC Genomics Workbench is a highly accurate and com- • Genotype SNP markers with high sensitivity and speci-
prehensive desktop NGS data analysis platform. It provides ficity through advanced visualization
user-friendly and customizable bioinformatics pipelines for
• Analysis of Unique Molecular Indexed panel data
SNPs, mitochondrial DNA analysis and other NGS applica-
avoids interpretation issues due to stochastic PCR effects
tions in human identity. For those with higher throughput
requirements, we can also provide local server and cloud • Flexible Import and Export possibilities enables seamless

solutions. integration of downstream analysis and statistics tools

• Dedicated HID plug-in tools for specialized analysis

(e.g., AQME mitochondrial DNA plug-in)

Visit QIAGEN Digital Insights for information on the CLC Genomics Workbench.
https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-
and-visualization/qiagen-clc-genomics-workbench/

8  Massively Parallel Sequencing Solutions for Human Identity 09/2020

Custom
Bioinformatics Services

The QIAGEN Digital Insights Bioinformatics Services team is dedicated to helping your organization achieve maximum
value from its data. We provide a comprehensive suite of consulting, software development, training and other professional
services that match bioinformatics and integration requirements regardless of complexity or scale. We have built this orga-
nization to help your organization achieve its scientific, IT and business goals because we realize that every organization
has unique needs.

Visit QIAGEN Digital Insights for more information.

https://digitalinsights.qiagen.com/services-overview

Ordering Information
QIAseq Investigator panels

Catalog no. Panel name Total number of primers* Product no.

CDHS-15861Z-2897 ICMP Missing Persons SNP Panel 2897 333525

CDHS-11454Z-318 ID SNP Panel 318 333525

CDHS-12534Z-204 Global Ancestry SNP Panel 204 333525

CDHS-12533Z-169 Middle East Ancestry Panel 169 333525

DHS-105Z Human Mitochondria Whole Genome Panel 222 333502

(12)
DHS-105Z Human Mitochondria Whole Genome Panel 222 333505
(96)
CDHS-13743-27 Human Mitochondria Control Region Panel 27 333525

Inquire Microhaplotype Panel Inquire

*The number of primers in a panel is represented by the last digits of the catalog number. For example, a custom panel with catalog number CDHS-
00100Z-1256 has 1256 primers.

Massively Parallel Sequencing Solutions for Human Identity 09/2020  9

Ordering Information

Products

Product Contents Cat. no.

QIAseq panels
QIAseq Targeted DNA Custom ALL reagents (except indexes) for targeted DNA sequencing; 333525
Panel (96) Custom panel for 96 samples
QIAseq Targeted DNA Panel (12) ALL reagents (except indexes) for targeted DNA sequencing; 333502
fixed panel for 12 samples; less than 200 genes
QIAseq Targeted DNA Panel (96) ALL reagents (except indexes) for targeted DNA sequencing; 333505
fixed panel for 96 samples; less than 200 genes
Indexes/adaptors: Illumina platform
QIAseq 12-Index I (48) Box containing molecularly-indexed adapters and primers, 333714
enough for a total of 48 samples – for indexing up to 12
samples for targeted panel sequencing on Illumina platforms
QIAseq 96-Index I Set A (384) Box containing molecularly-indexed adapters and primers, 333727
enough for a total of 384 samples – for indexing up to 96
samples for targeted panel sequencing on Illumina platforms;
one of 4 sets required for multiplexing 384 samples
QIAseq 96-Index I Set B (384) Box containing molecularly-indexed adapters and primers, 333737
enough for a total of 384 samples – for indexing up to 96
samples for targeted panel sequencing on Illumina platforms;
2 of 4 sets required for multiplexing 384 samples
QIAseq 96-Index I Set C (384) Box containing molecularly-indexed adapters and primers, 333747
enough for a total of 384 samples – for indexing up to 96
samples for targeted panel sequencing on Illumina platforms;
3 of 4 sets required for multiplexing 384 samples
QIAseq 96-Index I Set D (384) Box containing molecularly-indexed adapters and primers, 333757
enough for a total of 384 samples – for indexing up to 96
samples for targeted panel sequencing on Illumina platforms;
4 of 4 sets required for multiplexing 384 samples
Indexes/adaptors: Ion Torrent platform
QIAseq 12-Index L (48) Box containing molecularly-indexed adapters and primers, 333764
enough for a total of 48 samples – for indexing up to 12 samples
for targeted panel sequencing on Ion Torrent platforms
QIAseq 96-Index L (384) Box containing molecularly-indexed adapters and primers in 333777
arrays, enough for a total of 384 samples – for indexing up
to 96 samples for targeted panel sequencing on Ion Torrent
platforms

see next page for a continued list

10  Massively Parallel Sequencing Solutions for Human Identity 09/2020

Ordering Information – continued
Product Contents Cat. no.
Quantification reagents
QIAseq DNA QuantiMIZE Array Kit qPCR arrays for optimizing amount of input DNA and PCR 333404
cycling conditions for low-quantity DNA samples DNAQA-002-xxx*

QIAseq Library Quant Array Kit Reagents for quantification of libraries prepared for Illumina 333304
platform; array format QSIL-003-xxx*
QIAseq Library Quant Array Kit Reagents for quantification of libraries prepared for Ion 333304
Torrent platform; array format QSIT-003-xxx*
Analysis
CLC Genomics Workbench, 1-year subscription for a static license to use the software 832021
Desktop Plus on a single computer; includes maintenance, upgrade
and service
CLC Custom Solutions, days Professional services 832580

* Value of “xxx” depends on cycler format.

Massively Parallel Sequencing Solutions for Human Identity 09/2020  11

 For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user
manual. QIAGEN kit handbooks and user manuals are available at www.qiagen.com or can be requested from QIAGEN
Technical Services or your local distributor.

Trademarks: QIAGEN®, Sample to Insight®, QIAseq®, Investigator® (QIAGEN Group); MiSeq® (Illumina, Inc.). Registered names, trademarks, etc. used in this document, even when not specifically marked as such, are not
to be considered unprotected by law.
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