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Chapter 21: Sex Chromosome Haplotyping and Gender Identification

21.1: Y Chromosome Haplotyping

Human Y Chromosome Genome

  • Patrilineage: The Y chromosome is inherited from the father and is passed on to all male offspring.

  • Pseudoautosomal Regions (PARs): Homologous nucleotide sequences that are present on the X and Y chromosomes.

    • PAR1: It is located on the terminal region of the short arm. It comprises 2.6 Mb. Twenty-four genes have been identified within the PAR1.

    • PAR2: It is located at the tip of the long arm. It comprises 320 kb, with only four genes identified so far.

  • Male-Specific Y Region: The remainder of the Y chromosome.

  • Polymorphic Sequences

    • DYF155S1: The first characterized VNTR at the human Y chromosome.

    • It consists of an array of AT-rich repeats at 25 bp per unit repeat.

Human family pedigree showing inheritance of the Y chromosome. Females and males are denoted by circles and squares, respectively. Red symbols indicate individuals who inherited the same Y chromosome.

Human Y chromosome structure.

Y-STR

  • Y-STRs used in forensic DNA testing are male specific and are thus useful in the investigation of sexual assault cases involving male suspects.

  • The technique can be used for paternity testing and the identification of missing persons.

  • The major disadvantage of Y-STR loci is that their discriminating power is lower than that of autosomal loci. Because Y chromosome loci are linked, the product rule for statistical calculations for profile probability does not apply.

  • Haplotypes: Alleles of Y-STR loci linked or inherited together.

  • In 1997, the European minimal haplotype locus set, also known as the minimal haplotype loci, was recommended by the International Y-STR User Group for forensic applications.


21.2: X Chromosome Haplotyping

  • X-chromosomal STR (X-STR) profiling is a useful tool in kinship testing in forensic investigations.

  • Homologous recombination between the X and Y chromosomes is restricted to the homologous PARs.

  • The paternal X chromosome is inherited by daughters as haplotypes.

  • Homologous recombination can occur between two X chromosomes in the mother– child transmission.

  • Recombination Fraction: The percentage of recombinants resulting from chromosomal crossover between two loci during meiosis among all the offspring.


21.3: Sex Typing for Gender Identification

Amelogenin Locus

  • This region encodes extracellular matrix proteins involved in tooth enamel formation.

  • Amelogenesis Imperfecta: A disorder that causes abnormal formation of tooth enamel in both primary and permanent teeth.

  • The AMEL locus has two homologous genes:

    • AMEL X: AMEL locus which is located on the human X chromosome.

    • AMEL Y: AMEL locus which is located on the human Y chromosome.

Structure of human AMELY gene.

Sex typing using AMEL markers. A 6-bp deletion in intron 3 is present in AMELX but not in AMELY and can be resolved using electrophoresis as described in the text.

Other Loci

  • Sex-determining region Y (SRY) gene: Encodes a transcription factor that plays a role in the regulation of sex determination toward male development.

    • The SRY protein contains a DNA-binding domain known as the HMG box.

    • SOX3: An SRY-related HMG box-containing gene, has been identified at Xq27.1 of the X chromosome, which shares sequence homology with SRY.

  • TSPY Locus: It encodes the testis-specific protein Y-encoded gene that is only expressed in the testis and may play a role in spermatogenesis.

    • DYS14: A marker utilized for the characterization of the TSPY locus.

    • TSPY-like (TSPYL) gene: It has been identified on the short arm of the X chromosome and is designated as TSPYL2.

    • TSPYL2: A single-copy gene per X chromosome and is 6.3 kb in length, consisting of 7 exons and 6 introns.

  • DXYS156: A polymorphic pentanucleotide STR. It is located at the pseudo-autosomal region of both X and Y chromosomes, is another candidate marker used for sex typing.

    • DXYS156 Y: Alleles that have an additional adenine insertion in the repeat units of STR.

  • Steroid sulfatase (STS) gene: Encodes an enzyme that catalyzes the conversion of sulfated steroid precursors to biologically active steroids such as estrogens and androgens.

MA

Chapter 21: Sex Chromosome Haplotyping and Gender Identification

21.1: Y Chromosome Haplotyping

Human Y Chromosome Genome

  • Patrilineage: The Y chromosome is inherited from the father and is passed on to all male offspring.

  • Pseudoautosomal Regions (PARs): Homologous nucleotide sequences that are present on the X and Y chromosomes.

    • PAR1: It is located on the terminal region of the short arm. It comprises 2.6 Mb. Twenty-four genes have been identified within the PAR1.

    • PAR2: It is located at the tip of the long arm. It comprises 320 kb, with only four genes identified so far.

  • Male-Specific Y Region: The remainder of the Y chromosome.

  • Polymorphic Sequences

    • DYF155S1: The first characterized VNTR at the human Y chromosome.

    • It consists of an array of AT-rich repeats at 25 bp per unit repeat.

Human family pedigree showing inheritance of the Y chromosome. Females and males are denoted by circles and squares, respectively. Red symbols indicate individuals who inherited the same Y chromosome.

Human Y chromosome structure.

Y-STR

  • Y-STRs used in forensic DNA testing are male specific and are thus useful in the investigation of sexual assault cases involving male suspects.

  • The technique can be used for paternity testing and the identification of missing persons.

  • The major disadvantage of Y-STR loci is that their discriminating power is lower than that of autosomal loci. Because Y chromosome loci are linked, the product rule for statistical calculations for profile probability does not apply.

  • Haplotypes: Alleles of Y-STR loci linked or inherited together.

  • In 1997, the European minimal haplotype locus set, also known as the minimal haplotype loci, was recommended by the International Y-STR User Group for forensic applications.


21.2: X Chromosome Haplotyping

  • X-chromosomal STR (X-STR) profiling is a useful tool in kinship testing in forensic investigations.

  • Homologous recombination between the X and Y chromosomes is restricted to the homologous PARs.

  • The paternal X chromosome is inherited by daughters as haplotypes.

  • Homologous recombination can occur between two X chromosomes in the mother– child transmission.

  • Recombination Fraction: The percentage of recombinants resulting from chromosomal crossover between two loci during meiosis among all the offspring.


21.3: Sex Typing for Gender Identification

Amelogenin Locus

  • This region encodes extracellular matrix proteins involved in tooth enamel formation.

  • Amelogenesis Imperfecta: A disorder that causes abnormal formation of tooth enamel in both primary and permanent teeth.

  • The AMEL locus has two homologous genes:

    • AMEL X: AMEL locus which is located on the human X chromosome.

    • AMEL Y: AMEL locus which is located on the human Y chromosome.

Structure of human AMELY gene.

Sex typing using AMEL markers. A 6-bp deletion in intron 3 is present in AMELX but not in AMELY and can be resolved using electrophoresis as described in the text.

Other Loci

  • Sex-determining region Y (SRY) gene: Encodes a transcription factor that plays a role in the regulation of sex determination toward male development.

    • The SRY protein contains a DNA-binding domain known as the HMG box.

    • SOX3: An SRY-related HMG box-containing gene, has been identified at Xq27.1 of the X chromosome, which shares sequence homology with SRY.

  • TSPY Locus: It encodes the testis-specific protein Y-encoded gene that is only expressed in the testis and may play a role in spermatogenesis.

    • DYS14: A marker utilized for the characterization of the TSPY locus.

    • TSPY-like (TSPYL) gene: It has been identified on the short arm of the X chromosome and is designated as TSPYL2.

    • TSPYL2: A single-copy gene per X chromosome and is 6.3 kb in length, consisting of 7 exons and 6 introns.

  • DXYS156: A polymorphic pentanucleotide STR. It is located at the pseudo-autosomal region of both X and Y chromosomes, is another candidate marker used for sex typing.

    • DXYS156 Y: Alleles that have an additional adenine insertion in the repeat units of STR.

  • Steroid sulfatase (STS) gene: Encodes an enzyme that catalyzes the conversion of sulfated steroid precursors to biologically active steroids such as estrogens and androgens.