<scp>SNP</scp> Miniplexes for Individual Identification of Random‐Bred Domestic Cats

Brooks, Brandon; Creighton, K B S Erica; Gandolfi, Barbara; Khan, B S Razib; Grahn, Robert A.; Lyons, Leslie A.

doi:10.1111/1556-4029.13026

Cited by 12 publications

(8 citation statements)

References 65 publications

(91 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2018) and were also mostly included in the SNP panel used in forensic applications (Brooks et al . 2016). These 109 SNPs and the SNPs of datasets B and C were prioritized for selection in the SNP panel under development and described here.…”

Section: Methodsmentioning

confidence: 99%

“…comm.). For cat SNP dataset A, a subset of SNPs selected were also included on the cat 63K array (109 of 148) (Gandolfi et al 2018) and were also mostly included in the SNP panel used in forensic applications (Brooks et al 2016). These 109 SNPs and the SNPs of datasets B and C were prioritized for selection in the SNP panel under development and described here.…”

Section: Candidate Snp Selectionmentioning

confidence: 99%

“…They result in high rates of individual identification and parental exclusion. In addition to routine applications, DNA profiling also plays an important role in forensic casework (Menotti-Raymond et al 1997;Kun et al 2013;Wictum et al 2013;Brooks et al 2016) and phylogenetic research (Lipinski et al 2008;Kurushima et al 2013;Sauther et al 2020).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus)

Groot¹,

Anderson²,

Bauer

et al. 2021

Animal Genetics

View full text Add to dashboard Cite

Summary The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. The International Society of Animal Genetics (ISAG) hosts the Applied Genetics in Companion Animals Workshop, which supports the standardization of genetic marker panels and genotyping for the identification of cats via comparison testing. SNP panels have been in development for many species, including the domestic cat. An ISAG approved core panel of SNPs for use in cat identification and parentage analyses is presented. SNPs (n = 121) were evaluated by different university‐based and commercial laboratories using 20 DNA samples as part of the ISAG comparison testing procedures. Different SNP genotyping technologies were examined, including DNA arrays, genotyping‐by‐sequencing and mass spectroscopy, to select a robust and efficient panel of 101 SNPs as the ISAG core panel for cats. The SNPs are distributed across all chromosomes including two on the X chromosome and an XY pseudo‐autosomal sexing marker (zinc‐finger XY; ZFXY). A population study demonstrated that the markers have an average polymorphic information content of 0.354 and a power of exclusion greater than 0.9999. The SNP panel should keep testing affordable while also allowing for the development of additional panels to monitor health, phenotypic traits, hybrid cats and highly inbred cats.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Candidate Snp Selectionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus)

Groot¹,

Anderson²,

Bauer

et al. 2021

Animal Genetics

View full text Add to dashboard Cite

show abstract

“…A fast and accurate SNP marker verification system running on an automated platform is needed as an alternative to existing verification systems based on MS markers [ 14 ]. Attempts to use a combination of SNP markers with automated platforms for target breed identification are being made for various varieties and in various fields [ 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs

Seo

Cho

Manjula

et al. 2021

Animals

View full text Add to dashboard Cite

A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array. Machine learning algorithms, a genome-wide association study (GWAS), linkage disequilibrium (LD) analysis, and principal component analysis (PCA) were used to distinguish a target (case) group for comparison with control chicken groups. In the processing of marker selection, a total of 47,303 SNPs were used for classifying chicken populations; 96 LD-pruned SNPs (50 SNPs per LD block) served as the best marker combination for target chicken classification. Moreover, 36, 44, and 8 SNPs were selected as the minimum numbers of markers by the AdaBoost (AB), Random Forest (RF), and Decision Tree (DT) machine learning classification models, which had accuracy rates of 99.6%, 98.0%, and 97.9%, respectively. The selected marker combinations increased the genetic distance and fixation index (Fst) values between the case and control groups, and they reduced the number of genetic components required, confirming that efficient classification of the groups was possible by using a small number of marker sets. In a verification study including additional chicken breeds and samples (12 lines and 182 samples), the accuracy did not significantly change, and the target chicken group could be clearly distinguished from the other populations. The GWAS, PCA, and machine learning algorithms used in this study can be applied efficiently, to determine the optimal marker combination with the minimum number of markers that can distinguish the target population among a large number of SNP markers.

show abstract

“…Documented court cases show that determining the origin of biological animal material (coat or blood) identified at the crime scene or on the clothing of suspects might serve as strong evidence throughout the crime investigation process. In such situations, demonstrating the origin of biological traces may be helpful in linking the crime to a specific individual and even indicate the perpetrator [3][4][5]. Forensic simulations with domestic animals witnessing burglaries and as-scene.…”

Section: Introductionmentioning

confidence: 99%

Preliminary analysis of polymorphism of STR markers in the population of domestic cats (Felis catus) in Lower Silesia

Cierzniak¹,

Jonkisz²,

Tokarski³

et al. 2018

amsik

View full text Add to dashboard Cite

Cel pracy: Badania genetyczne odgrywają niezwykle ważną rolę w procesie dochodzeniowym, stanowiąc często najistotniejszy dowód decydujący o rozstrzygnięciu sprawy. Mimo że większość analiz genetycznych przeprowadzanych w kryminalistyce dotyczy materiału ludzkiego, to identyfikacja genetyczna zwierząt staje się coraz powszechniejsza. Przebywające w otoczeniu człowieka zwierzęta domowe bywają niekiedy niemymi świadkami, a nawet obiektami działań przestępczych. Ich potencjalnie ograniczona rola dowodowa w takich sprawach może ulec zmianie dzięki możliwości wykorzystania zwierzęcych śladów pozostawionych na miejscu zbrodni. Tego rodzaju metody mogą stać się też wartościowym narzędziem w wielu innych dziedzinach. W ostatnich latach obserwuje się wzrost zainteresowania procesem ustalania wiarygodności pochodzenia zwierząt z określonej hodowli, przeciwdziałaniem kłusownictwu i nielegalnemu odstrzałowi zwierząt, np. chronionych żbików i rysi, a także nielegalnej sprzedaży zwierząt. Głównym celem przeprowadzonych badań była ocena stopnia polimorfizmu analizowanych markerów STR w kocim materiale genetycznym oraz określenie ich przydatności do stworzenia autorskiego testu na potrzeby identyfikacji genetycznej kotów. Materiał i metody: Przeprowadzone badania obejmowały analizę populacji kotów, która liczyła 123 niespokrewnione ze sobą osobniki reprezentujące różne rasy kotów domowych zamieszkujących teren Dolnego Śląska. Materiał w postaci kropli krwi lub wymazu z wewnętrznej strony policzka danego osobnika został poddany analizie pod kątem pięciu markerów STR za pomocą jednego testu typu multipleks (FCA742, FCA744, F124, FCA732, FCA749). Wyniki: Otrzymane wyniki dla każdego markera z osobna poddano analizie statystycznej i za pomocą testu χ 2 oceniono zgodność badanej populacji w zakresie danego markera z prawem Hardy' ego-Weinberga. Wnioski: Uzyskane wyniki wskazują na duży potencjał analizowanych markerów, pozwalający na wykorzystanie ich w badaniach identyfikacyjnych.

show abstract

SNP Miniplexes for Individual Identification of Random‐Bred Domestic Cats

Cited by 12 publications

References 65 publications

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus)

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus)

Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs

Preliminary analysis of polymorphism of STR markers in the population of domestic cats (Felis catus) in Lower Silesia

Contact Info

Product

Resources

About