Forensic DNA Analysis

Technological Development and Innovative Applications

Elena Pilli, Andrea Berti, Elena Pilli, Andrea Berti

• Publisher: Apple Academic Press
• Year: 2021
• ISBN:
  9781000064582
• Edition: 1
• Topic: Derecho
• Subtopic: Ciencias forenses

Forensic DNA Analysis: Technological Development and Innovative Applications provides a fascinating overview of new and innovative technologies and current applications in forensic genetics. Edited by two forensic experts with many years of forensic crime experience with the Italian police and with prestigious academic universities, the volume takes an interdisciplinary perspective, the volume presents an introduction to genome polymorphisms, discusses, forensic genetic markers, presents a variety of new methods and techniques in forensic genetics, and looks at a selection of new technological innovations and inventions now available from commercial vendors.

The book is an important resource for scientists, researchers, and other experts in the field who will find it of interest for its exhaustive discussion of the most important technological innovations in forensic genetics. For those newer to the field, the volume will be an invaluable reference guide to the forensic world.

PART I
Introduction to Genome Polymorphisms

CHAPTER 1

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DNA Polymorphisms and Genome Structure: Different Scales of Variation in the Human Genome

ANDREA NOVELLETTO*, and BIANCA MARIA CIMINELLI

Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy

*Corresponding author. E-mail: [email protected]

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ABSTRACT

Modern human genetic diversity is the result of mutation, selection, migration, admixture, isolation, and drift. In the latest years, hundreds of thousands of human genomes have been sequenced. We briefly discuss the main findings concerning the occurrence of three classes of variations, that is, single-nucleotide polymorphisms, short tandem repeats, and structural variants as reported in seminal works, and provide a short guide to browsers and databases to query these variants’ features. We discuss some key aspects of genetic variation as far as the molecular bases, quantitative impact, and population distribution are concerned. The availability of these immense catalogs is only the first step to work out the effects of interindividual differences in functional elements encoded in the genome.

1.1 INTRODUCTION

Modern human genetic diversity is the result of the emergence of new variants by mutation, demographic history of humanity as a whole, and selective effects that have acted to adapt different populations to their environments. Extant patterns of diversity at the global level are now considered mainly the legacy of an Out of Africa model for the evolution and dispersal of anatomically modern humans. On top of this, more local processes, such as migration, admixture, adaptation, isolation, and drift, have molded the genome pools of local human groups, generating a kaleidoscopic distribution of variants across space.

Human genetic diversity has been long explored at the protein level, characterizing individuals and populations for electrophoretically or serologi-cally detectable variants (Cavalli-Sforza et al., 1994). In just few decades of DNA sequencing, the milestone where approximately 0.1% of living humans will have had their genomes resequenced to some degree is being reached, whereas resequencing of the genomes of our ancestors and other hominins is reshaping our understanding of human history (Shendure et al., 2017). This has produced catalogs of genetic variants that are growing at a thrilling pace and are freely available to the scientific community. These variations can be of several types, from simple substitutions that do not affect sequence length, to those that result in minor length differences, to those that affect multiple genes and multiple chromosomes (Kitts et al., 2014). In this chapter, we discuss some key aspects of genetic variation as far as the molecular bases, quantitative impact, and population distribution are concerned. The immense bibliography produced on these issues in recent years prevents any comprehensive presentation of the works, and references in the text should be all considered illustrative. As recent as they can be, we gave preference to seminal reviews, and the reader will find therein indications for a wealth of additional readings.

Sequence variation is of scientific interest to a variety of disciplines. Population geneticists analyze genetic diversity to work out phenomena as diverse as the descent of human groups (including the introgression with archaic hominins [Sankararaman et al., 20141), and the effects, duration, and intensity of natural selection on different portions of the genome, possibly in response to specific environmental conditions (Itan et al., 2010; Brown 2012; Yi et al., 2010; Hancock et al., 2011; Perry 2014). Genetic mapping of Mendelian traits in humans could only be pursued by linking specific traits to genetic variations spontaneously present in segregating pedigrees (Strachan and Read, 2011). Historically, the need for an advancement in mapping human genes has been a main driver for improving the description of genetic variation in all parts of the genome. Additionally, the investigation of relationships between variation and phenotype leveraged the available catalogs of variants in at least three main lines: to analyze the association between variant alleles and phenotypes in cohorts of unrelated cases and controls, according to the so-called Genome-wide Association Study (GWAS) approach (Altshuler et al., 2008; Mackay et al., 2009; Rosenberg et al., 2010); to obtain a compilation of coding variants by sequencing of massive numbers of exomes (Lek et al., 2016); to establish precise relationships between the presence of specific variant alleles and the level of expression of genes in a large array of tissues (GTEx Consortium 2017).

Progress in the description of DNA variation has been heavily dependent on the scaling up of the power of typing technologies (including genotyping arrays, exome capture, and massive parallel sequencing). However, its impact on everyday practice would have been minor without a parallel development of proper and easily accessible and searchable catalogs. Different databases have been implemented, each tailored on the specific features of different types of variants. These have been now integrated into genome browsers that allow the visualization of the occurrence and organization of variants onto the genome reference sequence (see Table 1.1).

The main leap forward toward a genome-wide description of variation at the level of DNA sequence has been produced by the 1000 Genome Project (1KGP), launched to discover, genotype, and provide accurate haplotype information on all forms of human DNA polymorphism in multiple human populations. Specifically, the goal was to characterize over 95% of variants that have allele frequency of 1% or higher (the classical definition of polymorphism) in each of five major population groups (populations with ancestry from Europe, East Asia, South Asia, West Africa, and the Americas) (The 1000 Genomes Project Consortium 2010). During its performance, the Project has grown both in the number of populations (and hence subjects) and depth of sequencing, reaching 2504 subjects at a mean depth of 7.4x (The 1000 Genomes Project Consortium 2015). The results were reported separately for molecularly distinct sources of genetic variation. In the rest of this text we will keep this distinction, referring mainly to the results of this study.

1.2 SINGLE-NUCLEOTIDE POLYMORPHISMS (SNPS)

An SNP is a variation, typically of a single base position in DNA, in which the less common form (allele) has a frequency of at least 1% in the population (see above). Indeed, the acronym SNP has now been extended also to variants that have been observed in a single instance (singletons), variants consisting in change of more nucleotides in a row, and variants consisting in the presence/absence of one or a few nucleotides (small indels). The majority of SNPs are biallelic, that is, there is only a reference and an alternative base at the variable position. Only multiple mutational hits can generate SNPs with three or four allelic forms. Note that the reference allele is the base represented in the genome reference sequence and is not necessarily the most frequent or the ancestral allele. In order to identify the ancestral allele, a comparison with an outgroup (nonhuman) species is necessary to determine which allele is shared between the two. This may reveal that the ancestral allele is the reference, or the alternative, or, in some cases, a third allele not observed in humans.

TABLE 1.1 An Initial List of Browsers and Searchable Databases on Human Genetic Variation

Acronym	URL	Short Description
Browsers
NCBI Genome data viewer	https://www.ncbi.nlm.nih.gov/genome/gdv/	The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of eukaryotic RefSeq genome assemblies. It allows users to visualize different types of sequence-associated data in a genomic context.
Ensembl	http://www.ensembl.org/index.html	Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation, and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory functions, and collects disease data.
UCSC Genome browser	http://genome-euro.ucsc.edu/cgi-bin/hgGateway?redirect=manual	The UCSC genome browser provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks.
gnomAD	https://gnomad.broadinstitute.org/	The Genome Aggregation Database (gnomAD) is a coalition of investigators seeking to aggregate and harmonize exome and genome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.
Databases SNP
dbSNP	https://www.ncbi.nlm.nih.gov/snp	The Single-Nucleotide Polymorphism database is a public domain archive for a broad collection of simple genetic polymorphisms. This collection includes single- base nucleotide substitutions, small-scale multibase deletions or insertions (also called deletion and insertion polymorphisms or DIPs), and retroposable element insertions and microsatellite repeat variations.
STR
STRCAT	http://strcatteamerlich.org/	A catalog of STR variation using over 1000 individuals from the 1000 Genomes Project.
STRBase	https://strbase.nist.gov/index.htm https://strbase.nist.govily_strs.htm	Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles are included in this database.
SV
DGV	http://dgv.tcagca/dgv/app/home	A curated catalog of human genomic structural variation.
DB VAR	https://www.ncbi.nlm.nih.gov/dbvar	NCBI database for structural variation.
DECIPHER	https://decipher.Sanger.ac	DECIPHER (DatabasE of genomiC variation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database that incorporates a suite of tools designed to aid the interpretation of genomic variants.
mtDNA
EMPOP mtDNA database	https://empop.online/	The EMPOP database aims at the collection, quality control, and searchable presentation of mtDNA haplotypes from all over the world.
MITOMAP	https://www.mitomap.org//MITOMAP	MITOMAP reports published data on human mitochondrial DNA variation.
Y chromosome
YHRD	https://yhrd.org/	Generates reliable Y-STR haplotype frequency estimates for Y-STR haplotypes to be used in the quantitative assessment of matches in forensic and kinship casework. Assessment of male population stratification among worldwide populations as far as reflected by Y-STR and Y-SNP.
Other
ALFRED	https:/...