TriXY—Homogeneous genetic sexing of highly degraded forensic samples including hair shafts

Madel, Maria‐Bernadette; Niederstätter, Harald; Parson, Walther

doi:10.1016/j.fsigen.2016.09.001

Cited by 17 publications

(10 citation statements)

References 51 publications

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Section: Introductionmentioning

confidence: 99%

“…An alternative method of sex estimation involves the detection of DNA markers from the X-and Y-chromosome (Loreille et al, 2018;Madel et al, 2016;Salido et al, 1992;Skoglund et al, 2013). Historically the most prominent methods rely on the detection of the amelogenin gene family, which has isoforms on both the X-and Y-chromosome (AMELX and AMELY) (Ballantyne, 2013;Garvin et al, 2012;Madel et al, 2016). Other methods measure the relative number of Xand Y-chromosome reads from massively parallel sequencing runs of DNA retained in samples (Loreille et al, 2018;Mittnik et al, 2016;Skoglund et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel

Parker

Yip

Eerkens

et al. 2019

Journal of Archaeological Science

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Amelogenin genes are located on both X and Y sex chromosomes in humans and are a major focus of DNA-based sex estimation methods. Amelogenin proteins, AMELX_HUMAN and AMELY_HUMAN, are expressed in the tooth organ and play a major role in mineralization of enamel, the most taphonomically resistant, archaeologically persistent human tissue. We describe shotgun liquid chromatography mass spectrometry analysis of 40 enamel samples representing 25 individuals, including modern third molars and archaeological teeth from open-air contexts including permanent adult (400-7300 BP) and deciduous teeth (100-1000 BP). Peptides specific to the X-chromosome isoform of amelogenin were detected in all samples. Peptides specific to the sexually dimorphic Y-chromosome isoform were also detected in 26 samples from 13 individuals, across all time periods, including previously unsexed deciduous teeth from archaeological contexts. While the signal of each gene product can vary by more than an order of magnitude, we show close agreement between osteological and amelogenin-based sex estimation and thus demonstrate that the protein-based signal can reliably be obtained from open-air archaeological contexts dating to at least 7300 years ago. While samples with AMELY_HUMAN peptides are unambiguously male, samples with no AMELY_HUMAN signal may either be low signal male false negative samples or female samples. In order to estimate sex in these samples we developed a probability curve of female sex as a function of the logarithm of AMELX_HUMAN signal (p < 0.0001) using logistic regression. This is also the first demonstration using proteomics to estimate sex in deciduous teeth and pushes back the application of the method to teeth that are at least 7300 years old.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel

Parker

Yip

Eerkens

et al. 2019

Journal of Archaeological Science

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“…The TriXY-Homogeneous genetic sexing [74] is another method that can use ancient DNA specimens from archeological excavations and hair shafts. This method uses three amplicons of known X and Y single nucleotide polymorphism (SNP) markers: one on the X chromosome and two on the Y chromosome detected by PCR.…”

Section: Sex Analysis In Forensic Medicinementioning

confidence: 99%

Methods for Prenatal Sex Determination and Their Importance in Understanding and Prevention of Gender-Related Birth Defects

Ornoy¹,

Weinstein-Fudim²,

Ergaz³

2020

Childbirth

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Various hormones, chemicals, and teratogenic agents exhibit gender-related effects in utero as well as postnatally. Among such gender-specific teratogens are endocrine disruptors, especially phthalates that affect male gonads, diabetesinduced oxidative stress with more deleterious effects on male offspring, procarbazine-induced cleft palate affecting more male fetal rats compared to females, and VPA-induced autism-like behavior that affects differently males than females. Hence, there are many needs for the accurate determination of genetic gender. In newborn animals, the morphological methods that exist for sex determination (i.e., anogenital distance) are generally inaccurate. Hence, an accurate and simple method for the prenatal and early postnatal assessment of the genetic sex, prior to reliable evaluation from the external genitalia, is of utmost importance. Indeed, several methods have been developed for accurate assessment of genetic sex, which are discussed in this chapter. Findings from studies in our laboratory have shown that the method described by McFarlan et al. for the assessment of genetic sex in adult mice by PCR of Sly/Xlr genes can be reliably used for the genetic sex determination of any tissue, including embryos and fetuses, with an accuracy of about 100%.

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“…This technique is useful when only a small amount of DNA is available, which is insufficient for performing an accurate analysis. In medicine, real-time PCR is applied to the discovery of tumour cells, to the diagnosis of infectious diseases, and to a plethora of other predictive medicine and diagnostic tasks [29]; it is widely used for studying genomes in several bacteria and protists which cannot be cultured; in legal medicine and forensics it has been demonstrated to be crucial for analysing fingerprints and stains found at crime scenes [30,31].…”

Section: Introductionmentioning

confidence: 99%

A Novel Algorithm for Online Inexact String Matching and its FPGA Implementation

2019

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Accelerating inexact string matching procedures is of utmost importance when dealing with practical applications where huge amount of data must be processed in real time, as usual in bioinformatics or cybersecurity. Inexact matching procedures can yield multiple shadow hits, which must be filtered, according to some criterion, to obtain a concise and meaningful list of occurrences. The filtering procedures are often computationally demanding and are performed offline in a post-processing phase. This paper introduces a novel algorithm for Online Approximate String Matching (OASM) able to filter shadow hits on the fly, according to general purpose priority rules that greedily assign priorities to overlapping hits. An FPGA hardware implementation of OASM is proposed and compared with a serial software version. Even when implemented on entry level FPGAs, the proposed procedure can reach a high degree of parallelism and superior performance in time compared to the software implementation, while keeping low the usage of logic elements. This makes the developed architecture very competitive in terms of both performance and cost of the overall computing system.

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TriXY—Homogeneous genetic sexing of highly degraded forensic samples including hair shafts

Cited by 17 publications

References 51 publications

Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel

Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel

Methods for Prenatal Sex Determination and Their Importance in Understanding and Prevention of Gender-Related Birth Defects

A Novel Algorithm for Online Inexact String Matching and its FPGA Implementation

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