Application of droplet digital PCR in diagnosing of X monosomy in mares

Szczerbal, Izabela; Nowacka‐Woszuk, Joanna; Kopp-Kuhlman, Christine; Mackowski, Mariusz; Świtoński, M.

doi:10.1111/evj.13214

Cited by 10 publications

(8 citation statements)

References 23 publications

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“…In addition, the results obtained in male-female chimeras demonstrate that SNP-CNA analysis can also detect individuals carrying ECAX mosaicisms. This is an important point considering that 63,X/64,XX, the third most important sex-pair chromosomal alteration reported in this species (Bugno et al 2001), cannot be detected by using the molecular methods currently available (Anaya et al 2017;Szczerbal et al 2020). However, all the chimeric samples analyzed in this study showed similar percentages of each cell line (64,XX or 64,XY in this case).…”

Section: Discussionsupporting

confidence: 48%

“…Copy number alterations in horses have been diagnosed using different approaches, including karyotyping (Neuhauser et al 2019), in situ hybridization (Bugno et al 2007b), short tandem repeat (STR) allele counting using standard (Demyda-Peyrás et al 2014) or specific panels (Anaya et al 2017), and, more recently, droplet digital PCR (Szczerbal et al 2020). These techniques are expensive and/ or highly specific to a particular syndrome, making their integration into routine screening problematic.…”

Section: Introductionmentioning

confidence: 99%

“…2017), and, more recently, droplet digital PCR (Szczerbal et al . 2020). These techniques are expensive and/or highly specific to a particular syndrome, making their integration into routine screening problematic.…”

Section: Introductionmentioning

confidence: 99%

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Screening and detection of chromosomal copy number alterations in the domestic horse using SNP‐array genotyping data

et al. 2021

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Summary Chromosomal abnormalities are a common cause of infertility in horses. However, they are difficult to detect using automated methods. Here, we propose a simple methodology based on single nucleotide polymorphism (SNP)‐array data that allows us to detect the main chromosomal abnormalities in horses in a single procedure. As proof of concept, we were able to detect chromosomal abnormalities in 33 out of 268 individuals, including monosomies, chimerisms, and male and female sex‐reversions, by analyzing the raw signal intensity produced by an SNP array‐based genotyping platform. We also demonstrated that the procedure is not affected by the SNP density of the array employed or by the inbreeding level of the individuals. Finally, the methodology proposed in this study could be performed in an open bioinformatic environment, thus permitting its integration as a flexible screening tool in diagnostic laboratories and genomic breeding programs.

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Section: Discussionsupporting

confidence: 48%

Section: Introductionmentioning

confidence: 99%

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Screening and detection of chromosomal copy number alterations in the domestic horse using SNP‐array genotyping data

et al. 2021

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“…2019; Szczerbal et al . 2020). The main goal of this study was thus to assess the usefulness of droplet digital PCR (ddPCR) in precise genotyping of equine STX17 4.6‐kb duplication, and to screen for its potential wider copy‐number variation in a panel of gray and nongray horses of various breeds.…”

Section: Figurementioning

confidence: 99%

The equine graying with age mutation of the STX17 gene: A copy number study using droplet digital PCR reveals a new pattern

et al. 2021

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Summary The equine graying with age causative mutation in the syntaxin‐17 gene (STX17) has been known for over a decade, but proper genotyping of this variant remains challenging due to its molecular character (4.6‐kb tandem duplication). Precise information on gray mutation status is important for horse breeders and veterinarians, since gray homozygous horses are more prone to developing aggressive melanoma tumors than heterozygotes. Since recent studies have confirmed that droplet digital PCR is a valuable technique for copy number analysis, we decided to investigate whether this method can be used for accurate genotyping of the horse graying‐related variant and established the copy numbers of the 4.6‐kb fragment in the available cohort (n = 75) of gray and nongray horses of various breeds. Surprisingly, we found that our STX17 genotype results varied from what has been previously published, suggesting that gray phenotype is associated with the presence of six (GG) or four (Gg) copies of studied region. All the examined nongray horses (gg) have the two copies of these fragments. This new pattern and its inheritance were also confirmed by an analysis conducted for the Polish Warmblood horse family. We noted no further copy number variation in the entire tested samples set. Our study confirmed the usefulness and accuracy of droplet digital PCR for genotyping STX17 gene variant. Further studies on a broader range of materials are needed to fully understand the origin and molecular structure of the graying causative mutation in the horse STX17.

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“…This increased prevalence observed, in comparison with other livestock species, is quite remarkable and mainly due to the complexity of the horse karyotype and the lack of availability of equine cytogenetic laboratories in several countries [42]. However, new genomic technology, based on short tandem repeats (STRs) [43], droplet digital PCR (ddPCR) [44], and, more recently, single nucleotide polymorphism (SNP) genotyping array [45], is being constantly developed. There is, therefore, likely to be an increase in the number and complexity of chromosomal syndromes associated with infertility detected in horses in the near future.…”

Section: Copy Number Abnormalities and Fertility: The Role Of The Sexmentioning

confidence: 99%

Impaired Reproductive Function in Equines: From Genetics to Genomics

Laseca

Anaya

Peña

et al. 2021

Animals

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Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.

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Application of droplet digital PCR in diagnosing of X monosomy in mares

Cited by 10 publications

References 23 publications

Screening and detection of chromosomal copy number alterations in the domestic horse using SNP‐array genotyping data

Screening and detection of chromosomal copy number alterations in the domestic horse using SNP‐array genotyping data

The equine graying with age mutation of the STX17 gene: A copy number study using droplet digital PCR reveals a new pattern

Impaired Reproductive Function in Equines: From Genetics to Genomics

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