Methods and Systems for Medical Sequencing Analysis

• US 20110098193A1
• Filed: 10/22/2010
• Published: 04/28/2011
• Est. Priority Date: 10/22/2009
• Status: Abandoned Application

• Current Assignee: National Center For Genome Resources
• Original Assignee: National Center For Genome Resources
• Inventors: Kingsmore, Stephen F., Bell, Callum J.
• Application Number:
  US12/910,764
• Publication Number:
  US 20110098193A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2545/113 with an external standard/control, i.e. control reaction is separated from the test/target reaction
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

Disclosed are methods of identifying elements associated with a trait, such as a disease. The methods can comprise, for example, identifying the association of a relevant element (such as a genetic variant) with a relevant component phenotype (such as a disease symptom) of the trait, wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait or disease, or a combination, wherein the relevant element is an element having a threshold value of importance of the element to homeostasis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination. The disclosed methods are based on a model of how elements affect complex diseases. The disclosed model is based on the existence of significant genetic and environmental heterogeneity in complex diseases. Thus, the specific combinations of genetic and environmental elements that cause disease vary widely among the affected individuals in a cohort. The disclosed model is an effective, general experimental design and analysis approach for the identification of causal variants in common, complex diseases by medical sequencing. Also disclosed herein are methods of identifying an inherited trait in a subject. The disclosed methods compare a reference sequence from a subject to a library of sequences that contain each mutation. For a given mutation, a normal sequence read aligns best to the normal library sequence. A read having the mutation aligns best to the mutant library sequence. The disclosed model and the disclosed methods based on the model can be used to generate valuable and useful information.

Claims

1. A method of identifying an inherited trait in a subject, comprising

collecting a biological sample from the subject comprising a DNA sequence;

aligning the DNA sequence to normal reference sequences and mutant reference sequences;

counting sequence reads aligning to normal references;

counting sequence reads aligning to mutant references; and

determining a ratio of aligned reads, wherein if the ratio is greater than a first value the inherited trait is a homozygous mutant, if the ratio is between a second value and a third value the inherited trait is a heterozygous mutant, and if the ratio is less than a fourth value the inherited trait is a homozygous wild-type.

2. The method of claim 1, wherein the first value is 86%, the second value is 18%, the third value is 14%, and the fourth value is 14%.

3. A method of determining a status of a subject with regard to an inherited trait comprising:

assaying an element from a sample from a subject to determine a subject DNA sequence;

comparing the subject DNA sequence to a set of DNA sequences by alignment wherein the set of DNA sequences comprises both normal, unaffected DNA sequences and mutated, variant DNA sequences;

identifying the element as being associated with the inherited trait by the coincidence of the element and the trait within the sample by determining a ratio of the subject DNA sequence that matches normal, unaffected DNA sequences and the mutated variant DNA sequences.

4. The method of claim 3, wherein the status can be unaffected and non-carrier of the inherited trait and/or unaffected and carrier of the inherited trait and/or affected and carrier of the inherited trait.

5. The method of claim 3, wherein the status of a predetermined number of inherited traits is determined from a sample.

6. The method of claim 3, wherein the inherited trait is a disease, a phenotype, a quantitative or qualitative trait, a disease outcome, a disease susceptibility, a biomarker, or a syndrome.

7. The method of claim 6, wherein the inherited trait is recessive, dominant, partially dominant, X-linked, complex, or multi-factorial.

8. The method of claim 3, where the sample is a blood sample, buccal smear, or biopsy.

9. The method of claim 3, wherein the assay of the element is performed by DNA sequencing.

10. The method of claim 3, wherein the element is a genetic element, wherein the type of element is a type of genetic variant, wherein the type of genetic element is a regulatory variant, a non-regulatory variant, a non-synonymous variant, a synonymous variant, a frameshift variant, a variant with a severity score at, above, or below a threshold value, a genetic rearrangement, a copy number variant, a gene expression difference, an alternative splice isoform, a deletion variant, an insertion variant, a transversion variant, an inversion variant, a translocation, or a combination thereof.

11. The method of claim 3, wherein the mutated, variant DNA sequences comprise a plurality of known variant sequences.

12. The method of claim 3, wherein the alignment is performed under conditions requiring a perfect match between the subject DNA sequence and a member of the reference set of DNA sequences.

13. The method of claim 3, wherein the element is a genetic element, wherein an amount of the element is a number of copies of the genetic element, the magnitude of expression of the genetic element, or a combination thereof.

14. The method of claim 3, wherein the comparing the subject DNA sequence to a set of DNA sequences by alignment comprises one or more of BLAST alignments, megaBLAST alignments, GMAP alignments, BLAT alignments, MAQ alignments, gSNAP alignments, or a combination thereof.

15. The method of claim 3, wherein the reference set of DNA sequences comprises one or more of the RefSeq genome database, the transcriptome database, the GENBANK database, or a combination thereof.

16. The method of claim 10, wherein the variant genetic elements are filtered to select candidate variant genetic elements, wherein the variant genetic elements are filtered by selecting variant genetic elements that are present in a threshold number of sequence reads, are present in a threshold percentage of sequence reads, are represented by a threshold read quality score at variant base(s), are present in sequence reads from in a threshold number of strands, are aligned at a threshold level to a reference sequence, are aligned at a threshold level to a second reference sequence, are variants that do not have biasing features bases within a threshold number of nucleotides of the variant, or a combination thereof.

17. A system for identifying an inherited trait in a subject, comprising

a memory;

and

a processor, coupled to the memory, configured for,

collecting a biological sample from the subject comprising a DNA sequence,

aligning the DNA sequence to normal reference sequences and mutant reference sequences,

counting sequence reads aligning to normal references,

counting sequence reads aligning to mutant references, and

determining a ratio of aligned reads, wherein if the ratio is greater than a first value the inherited trait is a homozygous mutant, if the ratio is between a second value and a third value the inherited trait is a heterozygous mutant, and if the ratio is less than a fourth value the inherited trait is a homozygous wild-type.

18. The system of claim 17, wherein the first value is 86%, the second value is 18%, the third value is 14%, and the fourth value is 14%.

19. The system of claim 17, wherein the comparing aligning the DNA sequence to normal reference sequences and mutant reference sequences comprises one or more of BLAST alignments, megaBLAST alignments, GMAP alignments, BLAT alignments, MAQ alignments, gSNAP alignments, or a combination thereof.

20. The system of claim 17, wherein the normal reference sequences and mutant reference sequences comprises one or more of the RefSeq genome database, the transcriptome database, the GENBANK database, or a combination thereof.