Kaarel Krjutškov
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View article: Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data
Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data Open
View article: Y-mer: A k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data
Y-mer: A k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data Open
Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low coverage sequence (ulcWGS) depth < 0.1x to be gained at target loci. Leveraging the recent advances in telomere-…
View article: Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens
Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens Open
Honey’s DNA mixture originates from various organisms like plants, arthropods, fungi, bacteria, and viruses. Conventional methods like melissopalynological analysis and targeted honey DNA metabarcoding offer a limited view of honey’s biolo…
View article: BinDel: Detecting Clinically Relevant Fetal Genomic Microdeletions Using Low‐Coverage Whole‐Genome Sequencing‐Based NIPT
BinDel: Detecting Clinically Relevant Fetal Genomic Microdeletions Using Low‐Coverage Whole‐Genome Sequencing‐Based NIPT Open
Objective Clinically pathogenic chromosomal microdeletions cause severe genetic disorders. Motivated by the absence of reliable screening of microdeletions during the first‐trimester screening, we developed BinDel, a software tool to deter…
View article: The DoGA consortium expression atlas of promoters and genes in 100 canine tissues
The DoGA consortium expression atlas of promoters and genes in 100 canine tissues Open
View article: Y-mer: A k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data
Y-mer: A k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data Open
Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low sequence (ulcWGS) depth < 0.1x to be gained at target loci. Leveraging the recent advances in telomere-to-telome…
View article: Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens
Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens Open
Honey’s DNA mixture originates from various organismal groups like plants, arthropods, fungi, bacteria, and viruses. Conventional methods like melissopalynological analysis and targeted honey DNA metabarcoding offer a limited view of honey…
View article: Effects of chemical <i>in vitro</i> activation versus fragmentation on human ovarian tissue and follicle growth in culture
Effects of chemical <i>in vitro</i> activation versus fragmentation on human ovarian tissue and follicle growth in culture Open
STUDY QUESTION What is the effect of the chemical in vitro activation (cIVA) protocol compared with fragmentation only (Frag, also known as mechanical IVA) on gene expression, follicle activation and growth in human ovarian tissue in vitro…
View article: Aging promotes accumulation of senescent and multiciliated cells in human endometrial epithelium
Aging promotes accumulation of senescent and multiciliated cells in human endometrial epithelium Open
STUDY QUESTION What changes occur in the endometrium during aging, and do they impact fertility? SUMMARY ANSWER Both the transcriptome and cellular composition of endometrial samples from women of advanced maternal age (AMA) are significan…
View article: Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human
Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human Open
Background Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiol…
View article: Effects of exercise on whole‐blood transcriptome profile in children with overweight/obesity
Effects of exercise on whole‐blood transcriptome profile in children with overweight/obesity Open
Background The current knowledge about the molecular mechanisms underlying the health benefits of exercise is still limited, especially in childhood. We set out to investigate the effects of a 20‐week exercise intervention on whole‐blood t…
View article: Targeted gene expression profiling for accurate endometrial receptivity testing
Targeted gene expression profiling for accurate endometrial receptivity testing Open
View article: Optimized single-cell RNA sequencing protocol to study early genome activation in mammalian preimplantation development
Optimized single-cell RNA sequencing protocol to study early genome activation in mammalian preimplantation development Open
View article: Aging affects ciliated cells development in the human endometrial epithelium
Aging affects ciliated cells development in the human endometrial epithelium Open
The twenties are typically considered the prime reproductive years for women. However, in today’s modern world, many women are choosing to delay family planning, resulting in an increase of females in their forties seeking fertility treatm…
View article: BinDel: detecting clinically relevant fetal genomic microdeletions using low-coverage whole-genome sequencing-based NIPT
BinDel: detecting clinically relevant fetal genomic microdeletions using low-coverage whole-genome sequencing-based NIPT Open
Background Clinically pathogenic chromosomal microdeletions (MDs) cause severe fetal genetic disorders such as DiGeorge and Prader-Willi/Angelman syndromes. Motivated by the absence of reliable blood and/or ultrasound screening biomarkers …
View article: Targeted gene expression profiling for accurate endometrial receptivity testing
Targeted gene expression profiling for accurate endometrial receptivity testing Open
STUDY QUESTION How accurately can a targeted gene expression sequencing assay estimate endometrial receptivity corresponding to the window of implantation? DESIGN Endometrial biopsies (n=175) from healthy fertile volunteers (n=66), polycys…
View article: DUX4 is a multifunctional factor priming human embryonic genome activation
DUX4 is a multifunctional factor priming human embryonic genome activation Open
View article: Prenatal diagnosis of a 46,XY karyotype female fetus with an SRY-associated gonadal dysgenesis, conceived through an intracytoplasmic sperm injection: a case report
Prenatal diagnosis of a 46,XY karyotype female fetus with an SRY-associated gonadal dysgenesis, conceived through an intracytoplasmic sperm injection: a case report Open
Background Permanent progression of paternal age and development of reproductive medicine lead to increase in number of children conceived with assisted reproductive techniques (ART). Although it is uncertain if ARTs have direct influence …
View article: Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo–endometrium interplay
Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo–endometrium interplay Open
STUDY QUESTION Which genes regulate receptivity in the epithelial and stromal cellular compartments of the human endometrium, and which molecules are interacting in the implantation process between the blastocyst and the endometrial cells?…
View article: Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples
Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples Open
Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are availab…
View article: Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog
Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog Open
View article: Dog colour patterns explained by modular promoters of ancient canid origin
Dog colour patterns explained by modular promoters of ancient canid origin Open
Distinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps r…
View article: Decidualized endometrial stromal cells present with altered androgen response in PCOS
Decidualized endometrial stromal cells present with altered androgen response in PCOS Open
View article: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
Small RNA expression and miRNA modification dynamics in human oocytes and early embryos Open
Small noncoding RNAs (sRNAs) play important roles during the oocyte-to-embryo transition (OET), when the maternal phenotype is reprogrammed and the embryo genome is gradually activated. The transcriptional program driving early human devel…
View article: Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion
Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion Open
The extracellular environment consists of a plethora of molecules, including extracellular miRNA that can be secreted in association with extracellular vesicles (EVs) or soluble protein complexes (non-EVs). Yet, interest in therapeutic sho…
View article: Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples
Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples Open
Motivation Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools …
View article: Nasal upregulation of<i>CST1</i>in dog-sensitised children with severe allergic airway disease
Nasal upregulation of<i>CST1</i>in dog-sensitised children with severe allergic airway disease Open
Background The clinical presentation of children sensitised to dog dander varies from asymptomatic to severe allergic airway disease, but the genetic mechanisms underlying these differences are not clear. The objective of the present study…
View article: Profiling of extracellular small RNAs highlights a strong bias towards non-vesicular secretion
Profiling of extracellular small RNAs highlights a strong bias towards non-vesicular secretion Open
Extracellular environment consists of a plethora of different molecules, including extracellular miRNA that can be secreted in association with extracellular vesicles (EVs) or soluble protein complexes (non-EVs). Yet, it is generally accep…
View article: Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes Open
To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip involving 34,840 cases and 114,981 controls, overwhelmingly of European de…
View article: Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing
Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing Open