Detection of human .alpha.-thalassemia mutations and their use as predictors of blood-related disorders

• US 5,750,345 A
• Filed: 10/31/1995
• Issued: 05/12/1998
• Est. Priority Date: 10/31/1995
• Status: Expired due to Term

• Current Assignee: Medifacts Systems, Inc.
• Original Assignee: Evanston Hospital Corporation (Quincy Health LLC)
• Inventors: Bowie, Lemuel J.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): SHOEMAKER, DEBRA GUNNERSEN
• Application Number:
  US08/550,715
• Time in Patent Office: 924 Days
• Field of Search: 435/6, 435/91.2, 935/8, 935/77, 935/78, 536/23.1, 536/23.5, 536/24.33
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The invention is based on the discovery that adults having a genotype comprising a hemoglobin α-gene deletion are significantly more likely to be hypertensive than adults having a normal (αα/αα) gentoype. The invention provides an improved method for determining a human subject'"'"'s genotype at the α-gene loci; a method of screening a human subject for an increased potential of developing hypertension and other blood-related disorders; and provides an apparatus/kit for screening a human subject for a risk of developing hypertension and other blood-related disorders.

Claims

1. A method of screening a human subject for an increased risk of developing a blood-related disorder, comprising the steps of:

(a) assaying genomic DNA of a human subject to determine a presence or an absence of an α

-globin deletion mutation; and

(b) screening for an increased risk of developing a blood-related disorder from the presence or absence of an α

-globin deletion mutation in said genomic DNA, wherein the presence of an α

-globin deletion mutation in the genomic DNA correlates with an increased risk of developing a blood-related disorder, and wherein said blood-related disorder is selected from the group consisting of hypertension, myocardial infarction, and diabetes.

2. The method of claim 1 wherein the human subject is normotensive and the blood-related disorder is hypertension.

3. The method of claim 2 wherein the α

-globin deletion mutation is selected from the group consisting of an -α

³.7 deletion, an MED deletion, an --SEA deletion, an -α

⁴.2 deletion, and an --BRIT deletion.

4. The method of claim 2 wherein the genomic DNA is assayed to determine the presence or the absence of an -α

³.7 deletion mutation.

5. The method of claim 4 wherein the human subject is heterozygous for an -α

³.7 deletion.

6. The method of claim 1 wherein said human subject has a genotype free of β

-globin mutations that cause deficient synthesis of normal β

-globin chains.

7. A method of screening for an increased potential for developing hypertension in a normotensive human individual comprising the steps of:

(a) isolating DNA from said human individual;

(b) assaying said DNA for the presence of a deletion relative to DNA of a normal human subject, said deletion comprising a reduction in the number of α

-globin genes in the genome of the normotensive human individual; and

(c) screening for an increased potential for developing hypertension in said normotensive human individual, wherein the presence of said deletion in the DNA isolated from the normotensive human individual is indicative of an increased potential for developing hypertension.

8. The method of claim 7 wherein the deletion is present in the DNA of the normotensive human individual.

9. The method of claim 7 wherein in step (b) said deletion is a deletion of at least 3.7 kilobases of DNA.

10. The method of claim 7 wherein the deletion is selected from the group consisting of an -α

³.7 deletion, an --MED deletion, an --SEA deletion, an -α

⁴.2 deletion, and an --BRIT deletion.

11. The method of claim 7 wherein step (b) comprises assaying said DNA for the presence of an -α

³.7 deletion relative to DNA of a normal human subject.

12. The method of claim 7 wherein step (b) comprises at least one of:

(i) determining a partial nucleotide sequence of the DNA from said human individual, said partial nucleotide sequence indicating the presence or absence of said deletion;

(ii) performing a restriction endonuclease digestion of the DNA from said human individual and a Southern hybridization, said Southern hybridization indicating the presence or absence of said deletion; and

(iii) performing a multiplex polymerase chain reaction with the DNA from said human individual to determine the presence or absence of said deletion.

13. The method of claim 7 wherein step (b) comprises performing a multiplex polymerase chain reaction with the DNA from said human individual to determine the presence or absence of said deletion.

14. The method of claim 7 wherein said human individual has a genotype free of β

-globin mutations that cause deficient synthesis of normal β

-globin chains.

15. A method for determining an increased potential for developing hypertension in a human individual comprising the steps of:

(a) isolating genomic DNA from said human individual;

(b) performing a multiplex polymerase chain reaction with said genomic DNA to amplify a marker portion and a control portion thereof, wherein the presence of an α

-globin gene deletion in said genomic DNA reduces the quantity of marker amplicons produced in the multiplex polymerase chain reaction relative to the quantity of control amplicons produced in said multiplex polymerase chain reaction; and

(c) determining a potential for developing hypertension from the quantity of marker amplicons relative to the quantity of control amplicons.

16. The method of claim 15 wherein step (c) further comprises the steps of:

(i) determining a ratio of marker amplicons to control amplicons produced in the multiplex polymerase chain reaction; and

(ii) comparing the ratio of step (i) to a ratio of marker amplicons to control amplicons produced in a multiplex polymerase chain reaction performed with genomic DNA of a normal human subject, wherein a lower marker amplicon to control amplicon ratio of step (i) indicates an increased potential for developing hypertension.

17. The method of claim 15 wherein step (b) further comprises the step of preparing a polymerase chain reaction solution, said solution comprising genomic DNA isolated from said human individual, a first pair of oligonucleotide primers for amplifying said marker portion of said DNA, and a second pair of oligonucleotide primers for amplifying said control portion of said DNA.

18. The method of claim 17 wherein said first pair of primers consists of a primer having the nucleotide sequence of SEQ ID NO:

4 and a primer having the nucleotide sequence of SEQ ID NO;

5.

19. The method of claim 18 wherein said second pair of primers consists of a primer having the nucleotide sequence of SEQ ID NO:

8 and a primer having the nucleotide sequence of SEQ ID NO;

9.

20. The method of claim 19 wherein in step (c) a marker amplicon to control amplicon ratio that is less than or equal to 0.6 is correlated with an increased potential for developing hypertension.

21. The method of claim 16 further comprising:

isolating genomic DNA from a normal human being;

performing a control multiplex polymerase chain reaction with the genomic DNA of the normal human being to amplify a marker portion and a control portion thereof; and

determining a ratio of marker amplicons to control amplicons produced in the control multiplex polymerase chain reaction;

wherein in step (ii), a lower marker amplicon to control amplicon ratio for the human individual compared to the ratio of marker amplicons to control amplicons for the normal human being indicates an increased potential for developing hypertension.

22. The method of claim 15 wherein said human individual has a genotype free of β

-globin mutations that cause deficient synthesis of normal β

-globin chains.

23. A method of determining an increased potential for developing a blood-related disorder, comprising the steps of:

(a) isolating genomic DNA from a human individual;

(b) assaying said DNA for a deletion relative to DNA of a normal human subject, said deletion reducing the number of α

-globin genes in the genome of the human individual; and

(c) determining an increased potential for developing a blood-related disorder in said human individual, wherein the presence of said deletion in the genomic DNA of the human individual is indicative of an increased potential for developing said blood-related disorder, said blood-related disorder selected from the group consisting of hypertension, myocardial infarction, and diabetes.

24. The method of claim 23 wherein said human individual has a genotype free of β

-globin mutations that cause deficient synthesis of normal β

-globin chains.

25. A kit comprising:

an assay means for assaying genomic DNA from a human subject for the presence of an α

-globin deletion mutation; and

a means for correlating the presence of an α

-globin deletion mutation to an increased potential of developing a blood-related disorder, said disorder selected from the group consisting of hypertension, myocardial infarction, and diabetes.

26. The kit of claim 25 wherein the assay means comprises a pair of α

-globin deletion-sensitive oligonucleotide primers.

27. The kit of claim 26 wherein the assay means further comprises first and second samples of human genomic DNA, said first sample having a homozygous normal α

-globin genotype, said second sample having a heterozygous α

α

/α

-globin-deletion genotype.

28. The kit of claim 27 wherein the second sample of human genomic DNA has a heterozygous α

α

/-α

³.7 α

genotype.

29. An assay for identifying a mild α

-thalassemia deletion genotype in a human individual comprising the steps of;

(a) providing genomic DNA from said human individual;

(b) performing a multiplex polymerase chain reaction with said genomic DNA to amplify a marker portion and a control portion thereof, wherein the presence of an α

-globin gene deletion in said genomic DNA reduces the quantity of marker amplicons produced in the multiplex polymerase chain reaction relative to the quantity of control amplicons produced in said multiplex polymerase chain reaction;

(c) determining a ratio of marker amplicons to control amplicons produced in the multiplex polymerase chain reaction;

(d) comparing the ratio of step (c) to a ratio of marker amplicons to control amplicons produced in a multiplex polymerase chain reaction performed with genomic DNA of a normal human subject; and

(e) identifying a mild α

-thalassemia deletion genotype in said human individual from said ratio of step (c), wherein a mild α

-thalassemia genotype in said individual correlates with a lower marker amplicon to control amplicon ratio of step (c) compared to the ratio of marker amplicons to control amplicons produced in a multiplex polymerase chain reaction performed with genomic DNA of a normal human subject.

30. An assay according to claim 29 for identifying an -α

³.7 α

/α

α

genotype in a human individual, wherein said marker portion of genomic DNA comprises a portion of chromosome 16 located between the α

2 and α

1 gene loci, and wherein in step (b), the presence of an -α

³.7 /α

α

genotype in said genomic DNA reduces the quantity of marker amplicons produced in the multiplex polymerase chain reaction relative to the quantity of control amplicons produced in said multiplex polymerase chain reaction.

31. An assay according to claim 29 for identifying an -α

⁴.2 α

/α

α

genotype in a human individual, wherein said marker portion of genomic DNA comprises a portion of chromosome 16 located 5'"'"' to the α

2 gene locus, and wherein in step (b), the presence of an -α

⁴.2 /α

α

genotype in said genomic DNA reduces the quantity of marker amplicons produced in the multiplex polymerase chain reaction relative to the quantity of control amplicons produced in said multiplex polymerase chain reaction.

32. An assay according to claim 29 wherein the marker amplicon to control amplicon ratio of step (c) is greater than zero.

33. The assay of claim 29 wherein in step (e) a mild α

-thalassemia deletion genotype is identified from a marker amplicon to control amplicon ratio of step (c) that is at least two standard deviations below the ratio of marker amplicons to control amplicons produced in multiplex polymerase chain reactions performed with genomic DNA of normal human subjects.

34. A method of determining a hypertension-correlated genetic disorder in a hypertensive human individual comprising the steps of:

(a) isolating DNA from said human individual;

(b) assaying said DNA for a deletion relative to DNA of a normal human subject, said deletion comprising a reduction in the number of α

-globin genes in the genome of the hypertensive human individual; and

(c) determining a presence of a hypertension-correlated genetic disorder in said individual from a presence of said deletion in said DNA.

35. A kit for determining the α

-globin genotype of a human individual comprising, in association;

a first pair of oligonucleotide primers for amplifying a first marker portion of a human chromosome 16, said first marker portion being absent from a human chromosome 16 having a single α

-gene deletion selected from the group consisting of an -α

³.7 deletion and an -α

⁴.2 deletion;

a second pair of oligonucleotide primers for amplifying a second marker portion of a human chromosome 16, said second marker portion being present in a human chromosome 16 having the single α

-gene deletion and being absent from a human chromosome 16 having an --MED deletion; and

a control pair of oligonucleotide primers for amplifying a control portion of human genomic DNA, wherein said first pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQ ID NO;

4 and a primer having the nucleotide sequence of SEQ ID NO;

5; and

wherein said second pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQ ID NO;

6 and a primer having the nucleotide sequence of SEQ ID NO;

7.

36. A kit for determining the α

-globin genotype of a human individual comprising, in association;

a first pair of oligonucleotide primers for amplifying a first marker portion of a human chromosome 16, said first marker portion being absent from a human chromosome 16 having an -α

³.7 deletion;

a second pair of oligonucleotide primers for amplifying a second marker portion of a human chromosome 16, said second marker portion being present in a human chromosome 16 having the single α

-gene deletion and being absent from a human chromosome 16 having an --MED deletion;

a third pair of oligonucleotide primers for amplifying a third marker portion of a human chromosome 16, said third marker portion being absent from a human chromosome 16 having an -α

⁴.2 deletion; and

a control pair of oligonucleotide primers for amplifying a control portion of human genomic DNA,

wherein said first pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQ ID NO;

4 and a primer having the nucleotide sequence of SEQ ID NO;

5;

wherein said second pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQ ID NO;

6 and a primer having the nucleotide sequence of SEQ ID NO;

7; and

wherein said third pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQ ID NO;

12 and a primer having the nucleotide sequence of SEQ ID NO;

13.

37. A kit for determining the α

-globin genotype of a human individual by multiplex polymerase chain reaction with genomic DNA of said individual, said kit comprising, in association;

a first pair of oligonucleotide primers for amplifying a first marker portion of a human chromosome 16, said first marker portion being absent from a human chromosome 16 having an -α

³.7 deletion wherein said first pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQUENCE ID NO;

4 and a primer having the nucleotide sequence of SEQUENCE ID NO;

5;

a second pair of oligonucleotide primers for amplifying a second marker portion of a human chromosome 16, said second marker portion being present in a human chromosome 16 having a single α

-gene deletion selected from the group consisting of an -α

³.7 deletion and an -α

⁴.2 deletion and being absent from a human chromosome 16 having an --MED deletion;

a third pair of oligonucleotide primers for amplifying a third marker portion of a human chromosome 16, said third marker portion being absent from a human chromosome 16 having an -α

⁴.2 deletion wherein said third pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQUENCE ID NO;

12 and a primer having the nucleotide sequence of SEQUENCE ID NO;

13; and

a control pair of oligonucleotide primers for amplifying a control portion of human genomic DNA,

said primer pairs permitting a determination, via multiplex polymerase chain reaction, of a -α

³.7 α

/α

α

mild α

-thalassemia genotype, a -α

⁴.2 α

/α

α

mild α

-thalassemia genotype, and α

-thalassemia trait genotypes wherein at least two α

-globin gene alleles have been deleted.

38. A kit according to claim 37 wherein said second pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQ ID NO:

6 and a primer having the nucleotide sequence of SEQ ID NO;

7.

39. A kit according to claim 38 wherein said control pair of oligonucleotide primers consists of a primer having the nucleotide sequence of SEQ ID NO:

8 and a primer having the nucleotide sequence of SEQ ID NO;

9.