Identification of gene associated with reading disability and uses therefor
The present invention relates to identification of a human gene, DCDC2 (MIM: 605755), associated with susceptibility for developing reading disability (RD), which is useful in identifying or aiding in identifying individuals at risk for developing RD, as well as for diagnosing or aiding in the diagnosis of RD.
1. A method of detecting, in a sample obtained from a human, a variant doublecortin domain containing 2 (DCDC2) gene that comprises an alteration that is:
a deletion in intron 2 comprising SEQ ID NO: 75;
or
an allele of the short tandem repeat region of intron 2 that comprises one of SEQ ID NO: 77-SEQ ID NO: 86,
comprising:
(a) combining the sample with a polynucleotide probe that hybridizes, under highly stringent conditions, to the variant DCDC2 gene, but not to a wild type DCDC2 gene, wherein the variant DCDC2 gene comprises an alteration that is:
a deletion in intron 2 comprising SEQ ID NO: 75
or
an allele of the short tandem repeat region of intron 2 that comprises one of SEQ ID NO: 77-SEQ ID NO: 86;
and
(b) determining whether hybridization occurs,
wherein the occurrence of hybridization indicates that the variant DCDC2 gene that comprises the alteration is present in the sample.
2. The method of claim 1 , wherein the deletion comprises SEQ ID NO: 75, wherein the polynucleotide probe hybridizes to intron 2 at the flanking base at the start of the deletion in intron 2 and at the flanking base at the end of the deletion in intron 2, wherein the flanking base at the start of the deletion is C and the flanking base at the end of the deletion is T.
3. The method of claim 1 , wherein the deletion is genotyped by allele-specific amplification with a combination of three primers: a universal or shared forward primer; a reverse primer for non-deleted chromosomes and a reverse primer for deleted chromosomes.
4. The method of claim 3 , wherein in (a), the sample is combined with a universal or shared forward primer of sequence:
AGCCTGCCTACCACAGAGAA;
(SEQ ID NO: 3)
a deletion reverse primer of sequence:
TGAAACCCCGTCTCTACTGAA;
(SEQ ID NO: 4)
and
a non-deletion reverse primer of sequence:
GGAACAACCTCACAGAAATGG.
(SEQ ID NO: 5)
5. A method of detecting, in a sample obtained from a human, a variant doublecortin domain containing 2 (DCDC2) gene that comprises an alteration that is:
a deletion in intron 2 comprising SEQ ID NO: 75;
or
an allele of the short tandem repeat region of intron 2 that comprises one of SEQ ID NO: 77-SEQ ID NO: 86,
comprising:
(a) combining the sample with a polynucleotide probe that hybridizes, under highly stringent conditions, to the variant DCDC2 gene that comprises:
a deletion in intron 2 comprising SEQ ID NO: 75;
or
an allele of the short tandem repeat region of intron 2 that comprises one of SEQ ID NO: 77-SEQ ID NO: 86,
thereby producing a combination;
(b) maintaining the combination produced in step (a) under highly stringent hybridization conditions; and
(c) comparing hybridization that occurs in the combination with hybridization in a control sample, wherein the control sample includes a polynucleotide probe that does not bind to the variant DCDC2 gene or binds only to a wild type DCDC2 gene, and the control sample is the same type of sample as in (a) and is treated the same as the sample in (a), and
wherein the occurrence of hybridization in the combination but not in the control sample indicates that the variant DCDC2 gene is present in the sample.
6. The method of claim 5 , wherein the extent of hybridization is determined in step (c).
7. A method of detecting, in a sample obtained from a human, a variant DCDC2 gene that comprises an alteration that is:
a deletion in intron 2 comprising SEQ ID NO: 75;
or
an allele of the short tandem repeat region of intron 2 of DCDC2 that comprises one of SEQ ID NO: 77-SEQ ID NO: 86,
comprising:
(a) combining the sample with a pair of polynucleotide primers, wherein the first polynucleotide primer hybridizes to one side of DNA that is present in the variant DCDC2 gene but not present in a wildtype DCDC2 gene and the second polynucleotide primer hybridizes to the other side of DNA that is present in the variant DCDC2 gene but not present in a wildtype DCDC2 gene;
(b) amplifying DNA in the sample, thereby producing amplified DNA;
(c) sequencing the amplified DNA; and
(d) detecting in the amplified DNA the presence of variant DCDC2 DNA,
whereby the variant DCDC2 gene is detected.