Identification of DNA fragments and structural variations

• US 9,514,272 B2
• Filed: 10/11/2012
• Issued: 12/06/2016
• Est. Priority Date: 10/12/2011
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Kermani, Bahram Ghaffarzadeh, Drmanac, Radoje, Alferov, Oleg
• Primary Examiner(s): Sims, Jason
• Application Number:
  US13/649,966
• Publication Number:
  US 20130096841A1
• Time in Patent Office: 1,517 Days
• Field of Search: None
• US Class Current: 1/1
• 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
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

Various short reads can be grouped and identified as coming from a same long DNA fragment (e.g., by using wells with a relatively low-concentration of DNA). A histogram of the genomic coverage of a group of short reads can provide the edges of the corresponding long fragment (pulse). The knowledge of these pulses can provide an ability to determine the haploid genome and to identify structural variations.

Claims

1. A method of detecting a structural variation in a genome of a sample from an organism, the method comprising:

providing a plurality of aliquots, each aliquot comprising nucleic acid molecules of the genome that have barcodes to track from which aliquot a nucleic acid molecule originates, wherein each of the plurality of aliquots includes less than a genomic equivalent of the genome of the organism;

sequencing a plurality of nucleic acid molecules in the plurality of aliquots to obtain sequences of the plurality of nucleic acid molecules and the barcodes;

receiving, at a computer system, sequence data from the sequencing the sequence data including sequences of at least one portion of each nucleic acid molecule of the plurality of nucleic acid molecules, wherein the sequence data includes the barcodes for tracking from which aliquot a sequence originates;

for each of the plurality of nucleic acid molecules;

aligning, with the computer system, at least one sequence of the nucleic acid molecule to a reference genome;

for each of the plurality of aliquots, calculating, with the computer system, a histogram for a first chromosomal region by;

identifying a respective group of sequences as being derived from a same fragment of DNA based on the barcodes of the respective group of sequences corresponding to a same aliquot, the same fragment including at least a portion of the first chromosomal region;

for each genomic position of a plurality of genomic positions within the first chromosomal region;

aggregating a number of instances that an aligned sequence of the respective group includes the genomic position;

comparing the histograms to identify a common increase or decrease in the histograms within a same window of the first chromosomal region as a location of the structural variation in the first chromosomal region of the genome of the organism.

2. The method of claim 1, wherein the structural variation is an insertion of a novel sequence, insertion of a sequence from a different chromosomal region of a different chromosome or a same chromosome, deletion, or inversion of a portion of the first chromosomal region.

3. The method of claim 1, further comprising:

identifying common increases and decreases in histograms of other chromosomal regions, wherein the first chromosomal region is identified as having a first decrease in the corresponding histograms;

correlating the first decrease in the first chromosomal region with a second increase in a second chromosomal region;

determining the first decrease and the second increase to be part of a same structural variation;

determining that the first chromosomal region and the second chromosomal region are proximal to each other in the genome of the organism.

4. The method of claim 3, wherein correlating the first decrease in the first chromosomal region with the second increase in the second chromosomal region includes:

determining a first value from a first number of fragments of DNA that include both the first decrease and the second increase; and

comparing the first value to a threshold to determine that a correlation does exist when the first value is greater than the threshold.

5. The method of claim 4, wherein comparing the first number to the threshold includes:

calculating a function of the first value to obtain a first result; and

comparing the first result to the threshold, wherein the function is a ratio of the first value divided by a total number of fragments used to determine the structural variations in the first and second chromosomal regions.

6. The method of claim 5, wherein the first value is a number of fragments of DNA that include both the first decrease and the second increase.

7. The method of claim 5, further comprising:

assigning a respective score to the first decrease and the second increase, wherein the score reflects a likelihood that the increase or decrease exists, wherein the first value is a weighted sum that accounts for the respective scores.

8. The method of claim 5, further comprising:

assigning a respective score to each fragment of DNA that is identified as including both the first decrease and the second increase, wherein the first value is a weighted sum that accounts for the respective scores.

9. The method of claim 3, wherein correlating the first decrease in the first chromosomal region with a second increase in the second chromosomal region includes:

determining a number of pairs of arms reads from a same nucleic acid molecule that have;

a first arm read that aligns to the first chromosomal region; and

a second arm read that aligns to the second chromosomal region; and

comparing the first number to a threshold to determine that a correlation does exist when the first number is greater than the threshold.

10. The method of claim 3, further comprising:

comparing the first number of fragments to one or more additional numbers of fragments of DNA that include both the first decrease and at least one other increase of at least one other chromosomal region.

11. The method of claim 3, further comprising:

correlating a third increase in a third chromosomal region with a fourth decrease in a fourth chromosomal region;

determining the third decrease and the fourth increase to be part of a same structural variation, wherein the structural variation is an insertion of the third chromosomal region into the fourth chromosomal region; and

determining that the third chromosomal region and the fourth chromosomal region are proximal to each other in the genome of the organism.

12. The method of claim 1, further comprising:

identifying that two sequences of a group of sequences are derived from the same fragment of DNA based on the two sequences being of opposite arm reads of a nucleic acid molecule.

13. The method of claim 1, wherein identifying the common increase or decrease as the location of the structural variation in the first chromosomal region of the genome of the organism includes:

calculating a measure of the common increase or decrease;

comparing the measure to a threshold; and

determining that a structural variation exits when the measure is greater than the threshold.

14. The method of claim 13, wherein calculating the measure of the common increase or decrease includes:

aggregating the histograms exhibiting the common increase or decrease of the first chromosomal region to obtain a total histogram, wherein the calculating the measure uses values from the total histogram.

15. The method of claim 13, wherein calculating a measure of the common increase or decrease includes:

obtaining a maximum value from one or more of the histograms;

obtaining a minimum value from one or more of the histograms;

calculating a difference between the maximum value and the minimum value; and

comparing the difference to a difference threshold to determine if a structural variation exists.

16. The method of claim 1, further comprising:

determining the window of the first chromosomal region for identifying the common increase or decrease.

17. The method of claim 1, further comprising:

determining when an aligned sequence of the respective group includes a particular genomic position by;

receiving two arms reads of the aligned sequence, the two arm reads being aligned to the reference genome; and

determining that the aligned sequence includes any genomic positions between the two arm reads.

18. The method of claim 1, wherein comparing the histograms to identify the common increase or decrease in the histograms within the same window of the first chromosomal region includes:

determining a genomic location of a pulse in a histogram;

identifying a beginning of the pulse as an increase in the histogram; and

identifying an end of the pulse as a decrease in the histogram.

19. The method of claim 18, wherein determining the genomic location of the pulse in a histogram includes:

determining a set of continuous genomic positions with histogram values above a detection threshold; and

identifying the set as a first pulse, wherein the beginning of the first pulse is associated with a first genomic position above the detection threshold and the end of the second pulse is associated with a last genomic position above the detection threshold.

20. The method of claim 19, wherein the nucleic acid molecules undergo an amplification prior to the sequencing.

21. The method of claim 20, wherein the detection threshold is a number between 0.5 and 2.

22. The method of claim 19, wherein determining the genomic location of the pulse in the histogram further includes:

combining the first pulse with a second pulse when the end of the first pulse is within a length threshold of the beginning of the second pulse.

23. The method of claim 19, wherein the determining the set of continuous genomic positions with histogram values above the detection threshold uses average histogram values that are an average of raw histogram values within a window, wherein a raw histogram value is the number of instances that an aligned sequence includes a particular genomic position.

24. The method of claim 23, further comprising:

before calculating the average histogram values, identifying genomic positions having raw histogram values below a minimum threshold; and

for any genomic position with a raw histogram value below the minimum threshold, setting the raw histogram value to zero.

25. The method of claim 18, further comprising:

identifying incorrectly aligned sequences in the first chromosomal region; and

removing the incorrectly aligned sequences from any corresponding histograms.

26. A computer product comprising a computer readable medium storing a plurality of instructions for controlling a computer system to perform an operation of detecting a structural variation in a genome of a sample from an organism, the instructions comprising:

receiving sequence data from a sequencing of a plurality of nucleic acid molecules of the sample, the sequence data including sequences of at least one portion of each nucleic acid molecule of the plurality of nucleic acid molecules, wherein the sequencing is performed by;

providing a plurality of aliquots, each aliquot comprising nucleic acid molecules of the genome that have barcodes to track from which aliquot a nucleic acid molecule originates, wherein each of the plurality of aliquots includes less than a genomic equivalent of the genome of the organism;

sequencing a plurality of nucleic acid molecules in the plurality of aliquots to obtain sequences of the plurality of nucleic acid molecules and the barcodes, wherein the sequence data includes the barcodes for tracking from which aliquot a sequence originates;

for each of the plurality of nucleic acid molecules;

aligning at least one sequence of the nucleic acid molecule to a reference genome;

for each of the plurality of aliquots, calculating a histogram for a first chromosomal region by;

identifying a respective group of sequences as being derived from a same fragment of DNA based on the barcodes of the respective group of sequences corresponding to a same aliquot, the same fragment including at least a portion of the first chromosomal region;

for each genomic position of a plurality of genomic positions within the first chromosomal region;

aggregating a number of instances that an aligned sequence of the respective group includes the genomic position;

comparing the histograms to identify a common increase or decrease in the histograms within a same window of the first chromosomal region

as a location of the structural variation in the first chromosomal region of the genome of the organism.

27. The computer product of claim 26, wherein the instructions further comprise:

identifying common increases and decreases in histograms of other chromosomal regions, wherein the first chromosomal region is identified as having a first decrease in the corresponding histograms;

correlating the first decrease in the first chromosomal region with a second increase in a second chromosomal region;

determining the first decrease and the second increase to be part of a same structural variation;

determining that the first chromosomal region and the second chromosomal region are proximal to each other in the genome of the organism.

28. The computer product of claim 27, wherein correlating the first decrease in the first chromosomal region with the second increase in the second chromosomal region includes:

determining a first value from a first number of fragments of DNA that include both the first decrease and the second increase; and

comparing the first value to a threshold to determine that a correlation does exist when the first value is greater than the threshold.

29. The computer product of claim 28, wherein comparing the first number to the threshold includes:

calculating a function of the first value to obtain a first result; and

comparing the first result to the threshold, wherein the function is a ratio of the first value divided by a total number of fragments used to determine the structural variations in the first and second chromosomal regions.

30. The computer product of claim 27, wherein correlating the first decrease in the first chromosomal region with a second increase in the second chromosomal region includes:

determining a number of pairs of arms reads from a same nucleic acid molecule that have;

a first arm read that aligns to the first chromosomal region; and

a second arm read that aligns to the second chromosomal region; and

comparing the first number to a threshold to determine that a correlation does exist when the first number is greater than the threshold.

31. The computer product of claim 27, wherein the instructions further comprise:

correlating a third increase in a third chromosomal region with a fourth decrease in a fourth chromosomal region;

determining the third decrease and the fourth increase to be part of a same structural variation, wherein the structural variation is an insertion of the third chromosomal region into the fourth chromosomal region; and

determining that the third chromosomal region and the fourth chromosomal region are proximal to each other in the genome of the organism.

32. The computer product of claim 26, wherein identifying the common increase or decrease as the location of the structural variation in the first chromosomal region of the genome of the organism includes:

calculating a measure of the common increase or decrease;

comparing the measure to a threshold; and

determining that a structural variation exits when the measure is greater than the threshold.

33. The computer product of claim 32, wherein calculating the measure of the common increase or decrease includes:

aggregating the histograms exhibiting the common increase or decrease of the first chromosomal region to obtain a total histogram, wherein the calculating the measure uses values from the total histogram.

34. The computer product of claim 32, wherein calculating a measure of the common increase or decrease includes:

obtaining a maximum value from one or more of the histograms;

obtaining a minimum value from one or more of the histograms;

calculating a difference between the maximum value and the minimum value; and

comparing the difference to a difference threshold to determine if a structural variation exists.

35. The computer product of claim 26, wherein the instructions further comprise:

determining when an aligned sequence of the respective group includes a particular genomic position by;

receiving two arms reads of the aligned sequence, the two arm reads being aligned to the reference genome; and

determining that the aligned sequence includes any genomic positions between the two arm reads.

36. The computer product of claim 26, wherein comparing the histograms to identify the common increase or decrease in the histograms within the same window of the first chromosomal region includes:

determining a genomic location of a pulse in a histogram;

identifying a beginning of the pulse as an increase in the histogram; and

identifying an end of the pulse as a decrease in the histogram.

37. The computer product of claim 36, wherein determining the genomic location of the pulse in a histogram includes:

determining a set of continuous genomic positions with histogram values above a detection threshold; and

identifying the set as a first pulse, wherein the beginning of the first pulse is associated with a first genomic position above the detection threshold and the end of the second pulse is associated with a last genomic position above the detection threshold.

38. The computer product of claim 37, wherein the determining the set of continuous genomic positions with histogram values above the detection threshold uses average histogram values that are an average of raw histogram values within a window, wherein a raw histogram value is the number of instances that an aligned sequence includes a particular genomic position, wherein the instructions further comprise:

before calculating the average histogram values, identifying genomic positions having raw histogram values below a minimum threshold; and

for any genomic position with a raw histogram value below the minimum threshold, setting the raw histogram value to zero.