Methods and systems for analyzing nucleic acid molecules
Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.
1. A method comprising
(a) obtaining a plurality of cell-free nucleic acid molecules that is obtained or derived from a subject;
(b) enriching the plurality of cell-free nucleic acid molecules for genomic regions associated with a set of phased variants to form a sequencing library, wherein the sequencing library comprises at least 150,000 evaluable sequencing fragments;
(c) obtaining sequencing data from the sequencing library for each of the at least 150,000 evaluable sequencing fragments;
(d) computer processing the sequencing data for each of the at least 150,000 evaluable sequencing fragments to align the sequencing data for each of the at least 150,000 evaluable sequencing fragments to a human reference genome;
(e) identifying one or more cell-free nucleic acid molecules of the plurality of cell-free nucleic acid molecules, wherein each of the identified one or more cell-free nucleic acid molecules comprises a plurality of phased variants relative to a sequence from the reference genome, wherein at least 10% of the one or more cell-free nucleic acid molecules comprises a first phased variant of the plurality of phased variants and a second phased variant of the plurality of phased variants that are separated by at least one nucleotide;
(f) determining (i) the number of evaluable sequencing fragments processed in (d) and (ii) the number of the one or more cell-free nucleic acid molecules that comprise the plurality of phased variants identified in (e); and
(g) determining a condition of the subject based at least in part on the number of molecules that comprise the plurality of phased variants as identified in (f);
wherein an evaluable sequencing fragment is a nucleic acid fragment that covers a region of the genome that comprises two or more predefined mutations from the set of phased variants, wherein the predefined mutations occur within 170 bp of each other in genomic space.
2. The method of claim 1 , wherein the two or more predefined mutations are single nucleotide variants.
3. The method of claim 1 , wherein the set of phased variants is selected based on phased variants identified in a tumor sample of the subject.
4. The method of claim 3 , wherein the tumor sample is a solid tumor sample.
5. The method of claim 1 , wherein (b) comprises using a set of nucleic acid probes to selectively capture cell-free nucleic acid molecules from genomic regions associated with the set of phased variants.
6. The method of claim 1 , further comprising performing targeted sequencing of tumor DNA and normal DNA of the subject.
7. The method of claim 1 , wherein the condition is a cancer.
8. The method of claim 7 , wherein (e) further comprises determining a cell-of-origin of the cancer of the subject based at least in part on the plurality of phased variants.
9. The method of claim 7 , wherein (e) further comprises detecting minimal residual disease of the cancer of the subject based at least in part on the plurality of phased variants.
10. The method of claim 7 , wherein (e) further comprises detecting a relapse of cancer.
11. The method of claim 7 , wherein the cancer comprises lymphoma.
12. The method of claim 7 , wherein the cancer comprises a solid tumor.
13. The method of claim 1 , wherein (d) comprises identifying (1) sequencing reads of the sequencing data comprising doublet phased variants having 2 phased variants within individual cell-free nucleic acid molecules and (2) sequencing reads of the sequencing data comprising triplet phased variants having 3 phased variants within individual cell-free nucleic acid molecules, and determining a phased-variant tumor fraction for doublet and triplet phased variants.
14. The method of claim 13 , wherein (d) comprises identifying (3) sequencing reads of the sequencing data comprising quadruplet phased variants having 4 phased variants within individual cell-free nucleic acid molecules, and determining a phased-variant tumor fraction for quadruplet phased variants.
15. The method of claim 1 , wherein the sequencing data is at a molecular depth of at least 5,000×.
16. The method of claim 1 , wherein (b) comprises enriching the plurality of cell-free nucleic acid molecules to form the sequencing library such that the sequencing library is enriched for phased variants by at least 7,500× as compared to a whole genome sequencing library.
17. The method of claim 1 , wherein (d) comprises identifying the one or more cell-free nucleic acid molecules comprising the plurality of phased variants with a limit of detection of less than 1 in 50,000 evaluable sequencing fragments.
18. The method of claim 1 , wherein (d) comprises identifying the one or more cell-free nucleic acid molecules comprising the plurality of phased variants with a specificity of at least 95%.
19. The method of claim 1 , wherein (b) comprises selectively amplifying the plurality of cell-free nucleic acid molecules for genomic regions associated with the set of phased variants.
20. The method of claim 19 , wherein (b) comprises using a set of nucleic acid primers to selectively amplify the plurality of cell-free nucleic acid molecules for genomic regions associated with the set of phased variants.
21. The method of claim 1 , wherein the method does not comprise performing barcode-mediated error suppression of the sequencing data.
22. The method of claim 1 , further comprising determining that the one or more cell-free nucleic acid molecules are derived from a sample associated with the condition based on performing a statistical model analysis of the identified one or more cell-free nucleic acid molecules.
23. The method of claim 1 , wherein the plurality of cell-free nucleic acid molecules is obtained or derived from a plasma sample of the subject.
24. The method of claim 1 , wherein the plurality of cell-free nucleic acid molecules is obtained or derived from a blood sample of the subject.
25. The method of claim 1 , wherein the plurality of cell-free nucleic acid molecules is obtained or derived from a serum sample of the subject.
26. The method of claim 1 , wherein the enriched plurality of cell-free nucleic acid molecules are from regions of aberrant somatic hypermutation.
27. The method of claim 1 , wherein the one or more cell-free nucleic acid molecules comprising a plurality of phased variants are molecules derived from mutational processes associated with hypermutation.
28. A method comprising:
(a) obtaining a plurality of cell-free nucleic acid molecules that is obtained or derived from a subject;
(b) enriching the plurality of cell-free nucleic acid molecules for genomic regions associated with at least 5% of the genomic regions set forth below to form a sequencing library, wherein the sequencing library comprises at least 150,000 evaluable sequencing fragments;
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106579000
106580000
chr14
106610000
106611000
chr14
106641000
106642000
chr14
106642000
106643000
chr14
106691000
106692000
chr14
106692000
106693000
chr14
106725000
106726000
chr14
106726000
106727000
chr14
106733000
106734000
chr14
106757000
106758000
chr14
106758000
106759000
chr14
106791000
106792000
chr14
106804000
106805000
chr14
106805000
106806000
chr14
106806000
106807000
chr14
106815000
106816000
chr14
106816000
106817000
chr14
106817000
106818000
chr14
106829000
106830000
chr14
106830000
106831000
chr14
106877000
106878000
chr14
106878000
106879000
chr14
106967000
106968000
chr14
106994000
106995000
chr14
106995000
106996000
chr14
107034000
107035000
chr14
107035000
107036000
chr14
107048000
107049000
chr14
107049000
107050000
chr14
107083000
107084000
chr14
107084000
107085000
chr14
107095000
107096000
chr14
107113000
107114000
chr14
107114000
107115000
chr14
107169000
107170000
chr14
107170000
107171000
chr14
107176000
107177000
chr14
107177000
107178000
chr14
107178000
107179000
chr14
107179000
107180000
chr14
107183000
107184000
chr14
107199000
107200000
chr14
107218000
107219000
chr14
107219000
107220000
chr14
107221000
107222000
chr14
107232000
107233000
chr14
107253000
107254000
chr14
107258000
107259000
chr14
107259000
107260000
chr15
45003000
45004000
chr15
45007000
45008000
chr15
45814000
45815000
chr15
59664000
59665000
chr15
65588000
65589000
chr15
78332000
78333000
chr15
83227000
83228000
chr15
86226000
86227000
chr15
86233000
86234000
chr15
86245000
86246000
chr16
368000
369000
chr16
3788000
3789000
chr16
10971000
10972000
chr16
10972000
10973000
chr16
10973000
10974000
chr16
10974000
10975000
chr16
11348000
11349000
chr16
11349000
11350000
chr16
21167000
21168000
chr16
27325000
27326000
chr16
27326000
27327000
chr16
27327000
27328000
chr16
27414000
27415000
chr16
29248000
29249000
chr16
31910000
31911000
chr16
46821000
46822000
chr16
50985000
50986000
chr16
64351000
64352000
chr16
78398000
78399000
chr16
78615000
78616000
chr16
78753000
78754000
chr16
78811000
78812000
chr16
79988000
79989000
chr16
81836000
81837000
chr16
85932000
85933000
chr16
85933000
85934000
chr16
85934000
85935000
chr16
85936000
85937000
chr16
88441000
88442000
chr17
3598000
3599000
chr17
17286000
17287000
chr17
21194000
21195000
chr17
29646000
29647000
chr17
38020000
38021000
chr17
43662000
43663000
chr17
56408000
56409000
chr17
56409000
56410000
chr17
57916000
57917000
chr17
57917000
57918000
chr17
62007000
62008000
chr17
62008000
62009000
chr17
63067000
63068000
chr17
65676000
65677000
chr17
69365000
69366000
chr17
70083000
70084000
chr17
74733000
74734000
chr17
75447000
75448000
chr17
75448000
75449000
chr17
76775000
76776000
chr17
80928000
80929000
chr17
80976000
80977000
chr18
2709000
2710000
chr18
3600000
3601000
chr18
12062000
12063000
chr18
27771000
27772000
chr18
28066000
28067000
chr18
30349000
30350000
chr18
36806000
36807000
chr18
37751000
37752000
chr18
38672000
38673000
chr18
42168000
42169000
chr18
51952000
51953000
chr18
52447000
52448000
chr18
52988000
52989000
chr18
54653000
54654000
chr18
60794000
60795000
chr18
60805000
60806000
chr18
60806000
60807000
chr18
60809000
60810000
chr18
60821000
60822000
chr18
60825000
60826000
chr18
60826000
60827000
chr18
60828000
60829000
chr18
60873000
60874000
chr18
60875000
60876000
chr18
60876000
60877000
chr18
60983000
60984000
chr18
60984000
60985000
chr18
60985000
60986000
chr18
60986000
60987000
chr18
60987000
60988000
chr18
60988000
60989000
chr18
61810000
61811000
chr18
63080000
63081000
chr18
63791000
63792000
chr18
63875000
63876000
chr18
64643000
64644000
chr18
65863000
65864000
chr18
66328000
66329000
chr18
70462000
70463000
chr18
73767000
73768000
chr18
76515000
76516000
chr18
76724000
76725000
chr18
76725000
76726000
chr19
1612000
1613000
chr19
2476000
2477000
chr19
10304000
10305000
chr19
10305000
10306000
chr19
10335000
10336000
chr19
10340000
10341000
chr19
10341000
10342000
chr19
16030000
16031000
chr19
16436000
16437000
chr19
20889000
20890000
chr19
21073000
21074000
chr19
21092000
21093000
chr19
23841000
23842000
chr19
29256000
29257000
chr19
44183000
44184000
chr19
50399000
50400000
chr19
53419000
53420000
chr20
15470000
15471000
chr20
23359000
23360000
chr20
23912000
23913000
chr20
46131000
46132000
chr20
49127000
49128000
chr20
49648000
49649000
chr20
61607000
61608000
chr21
21597000
21598000
chr21
23458000
23459000
chr21
24998000
24999000
chr21
26935000
26936000
chr21
35779000
35780000
chr21
38779000
38780000
chr21
43254000
43255000
chr21
44612000
44613000
chr21
45381000
45382000
chr21
46058000
46059000
chr22
19050000
19051000
chr22
20212000
20213000
chr22
20708000
20709000
chr22
21994000
21995000
chr22
22379000
22380000
chr22
22380000
22381000
chr22
22381000
22382000
chr22
22385000
22386000
chr22
22452000
22453000
chr22
22453000
22454000
chr22
22516000
22517000
chr22
22517000
22518000
chr22
22550000
22551000
chr22
22569000
22570000
chr22
22676000
22677000
chr22
22677000
22678000
chr22
22707000
22708000
chr22
22712000
22713000
chr22
22723000
22724000
chr22
22724000
22725000
chr22
22730000
22731000
chr22
22731000
22732000
chr22
22735000
22736000
chr22
22749000
22750000
chr22
22758000
22759000
chr22
22759000
22760000
chr22
22764000
22765000
chr22
23028000
23029000
chr22
23029000
23030000
chr22
23035000
23036000
chr22
23039000
23040000
chr22
23040000
23041000
chr22
23041000
23042000
chr22
23055000
23056000
chr22
23063000
23064000
chr22
23090000
23091000
chr22
23100000
23101000
chr22
23101000
23102000
chr22
23114000
23115000
chr22
23134000
23135000
chr22
23154000
23155000
chr22
23161000
23162000
chr22
23162000
23163000
chr22
23165000
23166000
chr22
23192000
23193000
chr22
23197000
23198000
chr22
23198000
23199000
chr22
23199000
23200000
chr22
23203000
23204000
chr22
23204000
23205000
chr22
23205000
23206000
chr22
23207000
23208000
chr22
23209000
23210000
chr22
23213000
23214000
chr22
23214000
23215000
chr22
23219000
23220000
chr22
23220000
23221000
chr22
23222000
23223000
chr22
23223000
23224000
chr22
23224000
23225000
chr22
23226000
23227000
chr22
23227000
23228000
chr22
23228000
23229000
chr22
23229000
23230000
chr22
23230000
23231000
chr22
23231000
23232000
chr22
23232000
23233000
chr22
23233000
23234000
chr22
23234000
23235000
chr22
23235000
23236000
chr22
23236000
23237000
chr22
23237000
23238000
chr22
23241000
23242000
chr22
23242000
23243000
chr22
23243000
23244000
chr22
23244000
23245000
chr22
23247000
23248000
chr22
23248000
23249000
chr22
23249000
23250000
chr22
23260000
23261000
chr22
23261000
23262000
chr22
23263000
23264000
chr22
23264000
23265000
chr22
23273000
23274000
chr22
23277000
23278000
chr22
23278000
23279000
chr22
23281000
23282000
chr22
23282000
23283000
chr22
23284000
23285000
chr22
23523000
23524000
chr22
23524000
23525000
chr22
27236000
27237000
chr22
29195000
29196000
chr22
29196000
29197000
chr22
31826000
31827000
chr22
32982000
32983000
chr22
39852000
39853000
chr22
39854000
39855000
chr22
43360000
43361000
chr22
47186000
47187000
chr22
47738000
47739000
chr22
50336000
50337000
chrX
228000
229000
chrX
1514000
1515000
chrX
1611000
1612000
chrX
12993000
12994000
chrX
12994000
12995000
chrX
13419000
13420000
chrX
27031000
27032000
chrX
32315000
32316000
chrX
32317000
32318000
chrX
33144000
33145000
chrX
33145000
33146000
chrX
33146000
33147000
chrX
41366000
41367000
chrX
42802000
42803000
chrX
48775000
48776000
chrX
48776000
48777000
chrX
64071000
64072000
chrX
67030000
67031000
chrX
80258000
80259000
chrX
81172000
81173000
chrX
87742000
87743000
chrX
87831000
87832000
chrX
88263000
88264000
chrX
88458000
88459000
chrX
92647000
92648000
chrX
93279000
93280000
chrX
94079000
94080000
chrX
104006000
104007000
chrX
104269000
104270000
chrX
106132000
106133000
chrX
113095000
113096000
chrX
115676000
115677000
chrX
124996000
124997000
chrX
125708000
125709000
chrX
128565000
128566000
chrX
129643000
129644000
chrX
134903000
134904000
chrX
140846000
140847000
chrX
143750000
143751000
chrX
145016000
145017000
(c) obtaining sequencing data from the sequencing library for each of the at least 150,000 evaluable sequencing fragments;
(d) computer processing the sequencing data for each of the at least 150,000 evaluable sequencing fragments to align the sequencing data for each of the at least 150,000 evaluable sequencing fragments to a human reference genome; and
(e) identifying one or more cell-free nucleic acid molecules of the plurality of cell-free nucleic acid molecules, wherein each of the identified one or more cell-free nucleic acid molecules comprises a plurality of phased variants relative to a sequence from the human reference genome, wherein at least 10% of the one or more cell-free nucleic acid molecules comprises a first phased variant of the plurality of phased variants and a second phased variant of the plurality of phased variants that are separated by at least one nucleotide; and
(f) determining a condition of the subject based at least in part on the plurality of phased variants;
wherein an evaluable sequencing fragment is a nucleic acid fragment that covers a region of the genome that comprises two or more predefined mutations from a set of phased variants, wherein the predefined mutations occur within 170 bp of each other in genomic space.
29. A method comprising:
(a) obtaining a plurality of cell-free nucleic acid molecules that is obtained or derived from a subject;
(b) enriching the plurality of cell-free nucleic acid molecules for genomic regions associated with at least 500 of the genomic regions set forth below to form a sequencing library, wherein the sequencing library comprises at least 150,000 evaluable sequencing fragments;
Chromo-
Region
Region
Chromo-
Region
Region
some
Start
End
some
Start
End
chr1
756000
757000
chr1
160616000
160617000
chr1
1963000
1964000
chr1
162711000
162712000
chr1
2052000
2053000
chr1
163684000
163685000
chr1
3789000
3790000
chr1
167598000
167599000
chr1
6613000
6614000
chr1
167599000
167600000
chr1
6614000
6615000
chr1
167600000
167601000
chr1
6661000
6662000
chr1
174333000
174334000
chr1
6662000
6663000
chr1
187263000
187264000
chr1
9129000
9130000
chr1
187283000
187284000
chr1
10894000
10895000
chr1
187892000
187893000
chr1
17019000
17020000
chr1
195282000
195283000
chr1
17231000
17232000
chr1
198591000
198592000
chr1
19935000
19936000
chr1
198608000
198609000
chr1
21091000
21092000
chr1
198609000
198610000
chr1
23885000
23886000
chr1
202004000
202005000
chr1
28408000
28409000
chr1
203273000
203274000
chr1
32373000
32374000
chr1
203274000
203275000
chr1
36722000
36723000
chr1
203275000
203276000
chr1
46576000
46577000
chr1
203276000
203277000
chr1
51965000
51966000
chr1
205780000
205781000
chr1
51978000
51979000
chr1
205781000
205782000
chr1
51983000
51984000
chr1
206283000
206284000
chr1
72393000
72394000
chr1
206286000
206287000
chr1
73719000
73720000
chr1
217044000
217045000
chr1
77315000
77316000
chr1
226924000
226925000
chr1
81306000
81307000
chr1
226925000
226926000
chr1
81527000
81528000
chr1
226926000
226927000
chr1
82009000
82010000
chr1
229974000
229975000
chr1
84106000
84107000
chr1
235131000
235132000
chr1
87524000
87525000
chr1
235141000
235142000
chr1
94551000
94552000
chr1
238787000
238788000
chr1
94552000
94553000
chr1
248088000
248089000
chr1
103696000
103697000
chr2
630000
631000
chr1
116979000
116980000
chr2
1484000
1485000
chr1
149784000
149785000
chr2
7991000
7992000
chr1
149821000
149822000
chr2
12173000
12174000
chr1
149857000
149858000
chr2
12175000
12176000
chr1
149858000
149859000
chr2
12249000
12250000
chr2
14113000
14114000
chr2
89145000
89146000
chr2
17577000
17578000
chr2
89146000
89147000
chr2
19253000
19254000
chr2
89153000
89154000
chr2
24802000
24803000
chr2
89155000
89156000
chr2
31478000
31479000
chr2
89156000
89157000
chr2
41728000
41729000
chr2
89157000
89158000
chr2
45404000
45405000
chr2
89158000
89159000
chr2
47923000
47924000
chr2
89159000
89160000
chr2
47944000
47945000
chr2
89160000
89161000
chr2
51360000
51361000
chr2
89161000
89162000
chr2
51655000
51656000
chr2
89162000
89163000
chr2
56565000
56566000
chr2
89163000
89164000
chr2
57800000
57801000
chr2
89164000
89165000
chr2
60779000
60780000
chr2
89165000
89166000
chr2
60780000
60781000
chr2
89166000
89167000
chr2
63802000
63803000
chr2
89169000
89170000
chr2
63827000
63828000
chr2
89184000
89185000
chr2
64319000
64320000
chr2
89185000
89186000
chr2
65593000
65594000
chr2
89196000
89197000
chr2
67002000
67003000
chr2
89197000
89198000
chr2
70315000
70316000
chr2
89214000
89215000
chr2
79502000
79503000
chr2
89246000
89247000
chr2
79644000
79645000
chr2
89247000
89248000
chr2
81818000
81819000
chr2
89248000
89249000
chr2
82310000
82311000
chr2
89266000
89267000
chr2
82948000
82949000
chr2
89291000
89292000
chr2
85335000
85336000
chr2
89292000
89293000
chr2
88905000
88906000
chr2
89326000
89327000
chr2
88906000
88907000
chr2
89327000
89328000
chr2
88907000
88908000
chr2
89442000
89443000
chr2
89052000
89053000
chr2
89443000
89444000
chr2
89065000
89066000
chr2
89476000
89477000
chr2
89066000
89067000
chr2
89513000
89514000
chr2
89095000
89096000
chr2
89521000
89522000
chr2
89127000
89128000
chr2
89533000
89534000
chr2
89128000
89129000
chr2
89534000
89535000
chr2
89129000
89130000
chr2
89544000
89545000
chr2
89130000
89131000
chr2
89545000
89546000
chr2
89131000
89132000
chr2
90259000
90260000
chr2
89132000
89133000
chr2
90260000
90261000
chr2
89133000
89134000
chr2
96809000
96810000
chr2
89137000
89138000
chr2
96810000
96811000
chr2
89138000
89139000
chr2
96811000
96812000
chr2
89139000
89140000
chr2
98611000
98612000
chr2
89140000
89141000
chr2
100757000
100758000
chr2
89141000
89142000
chr2
100758000
100759000
chr2
89142000
89143000
chr2
106144000
106145000
chr2
89143000
89144000
chr2
111878000
111879000
chr2
89144000
89145000
chr2
111879000
111880000
chr2
112305000
112306000
chr3
32023000
32024000
chr2
116234000
116235000
chr3
50128000
50129000
chr2
116439000
116440000
chr3
54913000
54914000
chr2
124697000
124698000
chr3
56074000
56075000
chr2
125235000
125236000
chr3
59577000
59578000
chr2
127538000
127539000
chr3
60351000
60352000
chr2
136874000
136875000
chr3
60356000
60357000
chr2
136875000
136876000
chr3
60357000
60358000
chr2
136996000
136997000
chr3
60358000
60359000
chr2
137082000
137083000
chr3
60359000
60360000
chr2
140951000
140952000
chr3
60389000
60390000
chr2
141335000
141336000
chr3
60392000
60393000
chr2
141770000
141771000
chr3
60395000
60396000
chr2
146445000
146446000
chr3
60404000
60405000
chr2
146446000
146447000
chr3
60436000
60437000
chr2
156443000
156444000
chr3
60437000
60438000
chr2
172590000
172591000
chr3
60477000
60478000
chr2
176581000
176582000
chr3
60485000
60486000
chr2
179880000
179881000
chr3
60515000
60516000
chr2
180358000
180359000
chr3
60535000
60536000
chr2
189285000
189286000
chr3
60602000
60603000
chr2
189432000
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(c) obtaining sequencing data from the sequencing library for each of the at least 150,000 evaluable sequencing fragments;
(d) computer processing the sequencing data for each of the at least 150,000 evaluable sequencing fragments to align the sequencing data for each of the at least 150,000 evaluable sequencing fragments to a human reference genome; and
(e) identifying one or more cell-free nucleic acid molecules of the plurality of cell-free nucleic acid molecules, wherein each of the identified one or more cell-free nucleic acid molecules comprises a plurality of phased variants relative to a sequence from the human reference genome, wherein at least 10% of the one or more cell-free nucleic acid molecules comprises a first phased variant of the plurality of phased variants and a second phased variant of the plurality of phased variants that are separated by at least one nucleotide; and
(f) determining a condition of the subject based at least in part on the plurality of phased variants;
wherein an evaluable sequencing fragment is a nucleic acid fragment that covers a region of the genome that comprises two or more predefined mutations from a set of phased variants, wherein the predefined mutations occur within 170 bp of each other in genomic space.
30. A method comprising:
(a) obtaining a plurality of cell-free nucleic acid molecules that is obtained or derived from a subject;
(b) enriching the plurality of cell-free nucleic acid molecules for genomic regions associated with at least 5% of the genomic regions set forth below to form a sequencing library, wherein the sequencing library comprises at least 150,000 evaluable sequencing fragments;
Chromo-
Region
Region
Chromo-
Region
Region
some
Start
End
some
Start
End
chr1
2306311
2306832
chr1
2489111
2489330
chr1
2334441
2334664
chr1
2489726
2489973
chr1
2334671
2335161
chr1
2491206
2491455
chr1
2488006
2488247
chr1
2492036
2492175
chr1
2493051
2493333
chr1
226923691
226925200
chr1
2494241
2494376
chr1
227842646
227842718
chr1
2494556
2494745
chr2
1652010
1652858
chr1
3547350
3547715
chr2
48027958
48028159
chr1
3747620
3747798
chr2
48059883
48060051
chr1
3800045
3800148
chr2
48065973
48066184
chr1
3800155
3800363
chr2
55237198
55237610
chr1
4472438
4472621
chr2
56149510
56150116
chr1
4476348
4476627
chr2
58520800
58521222
chr1
9784432
9784540
chr2
59821914
59822083
chr1
23885407
23885541
chr2
60773084
60773479
chr1
23885582
23885938
chr2
61118794
61118998
chr1
27059146
27059321
chr2
61145504
61145785
chr1
27101071
27101294
chr2
61148869
61149644
chr1
27101401
27101613
chr2
61441169
61441870
chr1
27105466
27105671
chr2
61719434
61719642
chr1
27106311
27106523
chr2
62934009
62934460
chr1
27106711
27106920
chr2
63217829
63218002
chr1
29069531
29070185
chr2
63335242
63335600
chr1
34404022
34404171
chr2
63631157
63631817
chr1
35472492
35472739
chr2
63826277
63826429
chr1
61553802
61554330
chr2
65258145
65258367
chr1
72334891
72335045
chr2
65593035
65593153
chr1
72335051
72335120
chr2
65593180
65593250
chr1
85733207
85733640
chr2
77746602
77746988
chr1
85736272
85736619
chr2
80801235
80801513
chr1
85741932
85742068
chr2
88906681
88906861
chr1
86591437
86591909
chr2
89127261
89127335
chr1
107866871
107867579
chr2
89127461
89127946
chr1
109649126
109649304
chr2
89128431
89128574
chr1
109822181
109822805
chr2
89131726
89132295
chr1
110561141
110561757
chr2
89140556
89140755
chr1
111441722
111442219
chr2
89140886
89141350
chr1
111715727
111715908
chr2
89157326
89157609
chr1
117078642
117078856
chr2
89157626
89158011
chr1
117086927
117087172
chr2
89158036
89158938
chr1
120457960
120459297
chr2
89158941
89159493
chr1
160319283
160319532
chr2
89159511
89161445
chr1
181452914
181453131
chr2
89161926
89162149
chr1
185833555
185833832
chr2
89162776
89163285
chr1
185972790
185973006
chr2
89163306
89163837
chr1
186062580
186062797
chr2
89163861
89164838
chr1
186083050
186083301
chr2
89164866
89165181
chr1
186143590
186143828
chr2
89165191
89165644
chr1
186158895
186159102
chr2
89184966
89185186
chr1
190067139
190068194
chr2
89185196
89185704
chr1
201038552
201038756
chr2
89196226
89196411
chr1
203274697
203275926
chr2
89196851
89197324
chr1
203276207
203276586
chr2
89214836
89215040
chr2
89246681
89246772
chr2
145278311
145278659
chr2
89246786
89246857
chr2
145692901
145693081
chr2
89246911
89247053
chr2
148680516
148680692
chr2
89247096
89247215
chr2
169781120
169781352
chr2
89247526
89247628
chr2
170101185
170101401
chr2
89247641
89247735
chr2
198950434
198951003
chr2
89247831
89248010
chr2
242793232
242793447
chr2
89265756
89265829
chr2
242794037
242794192
chr2
89265936
89266013
chr2
242794317
242794537
chr2
89291906
89291981
chr2
242794822
242795040
chr2
89292131
89292217
chr2
242800887
242801093
chr2
89442291
89442561
chr3
7620223
7620990
chr2
89442616
89443259
chr3
16419204
16419479
chr2
89475781
89476009
chr3
38180129
38180549
chr2
89476041
89476122
chr3
38181334
38181509
chr2
89544331
89544608
chr3
38181854
38182099
chr2
89544656
89544899
chr3
38182194
38182407
chr2
89976276
89976426
chr3
38182554
38182844
chr2
89986776
89987023
chr3
49397608
49397717
chr2
89987031
89987108
chr3
49397718
49397827
chr2
90025206
90025289
chr3
49399903
49400084
chr2
90025296
90025378
chr3
49405833
49406013
chr2
90025471
90025554
chr3
49412838
49413046
chr2
90077981
90078054
chr3
64547204
64547477
chr2
90078136
90078222
chr3
64579889
64580094
chr2
90078251
90078335
chr3
71551101
71551497
chr2
90121891
90122008
chr3
140281598
140281875
chr2
90122021
90122157
chr3
164730700
164730888
chr2
90212016
90212093
chr3
165548198
165548680
chr2
90212196
90212278
chr3
176750699
176750928
chr2
90249151
90249275
chr3
176767759
176767977
chr2
90249346
90249419
chr3
176769304
176769543
chr2
90259931
90260059
chr3
176771659
176771732
chr2
90260181
90260258
chr3
183209758
183209937
chr2
96809889
96810144
chr3
183210258
183210544
chr2
96810164
96810374
chr3
183272308
183272521
chr2
100758483
100758660
chr3
183273063
183273456
chr2
103148733
103148948
chr3
184580663
184580872
chr2
117951919
117952057
chr3
185146278
185146873
chr2
136872525
136872740
chr3
185197923
185198317
chr2
136874415
136874797
chr3
185236908
185237109
chr2
136874920
136875662
chr3
185446223
185446389
chr2
141245127
141245373
chr3
185538773
185538951
chr2
145162401
145162624
chr3
185697423
185697669
chr2
145187091
145187638
chr3
186714604
186715001
chr2
145270956
145271394
chr3
186782529
186782790
chr2
145275631
145275744
chr3
186783389
186784291
chr2
145275756
145276174
chr3
187440189
187440445
chr2
145278026
145278305
chr3
187442669
187442920
chr3
187443239
187443438
chr5
67590966
67591183
chr3
187446814
187447831
chr5
75913716
75914448
chr3
187449434
187449655
chr5
83258967
83259183
chr3
187451284
187451667
chr5
112176756
112176958
chr3
187460134
187460530
chr5
124079827
124080721
chr3
187460824
187461302
chr5
131825017
131825239
chr3
187461319
187461381
chr5
135381969
135382218
chr3
187461454
187461918
chr5
137801487
137801637
chr3
187461924
187462343
chr5
137801697
137801804
chr3
187462374
187462887
chr5
140208033
140208874
chr3
187462924
187462999
chr5
158527642
158528019
chr3
187463004
187463525
chr5
176522449
176522613
chr3
187463709
187463781
chr6
392760
392967
chr3
187463794
187464109
chr6
393090
393309
chr3
187619334
187619708
chr6
394815
395025
chr3
187660817
187661390
chr6
14117992
14118654
chr3
187957432
187957507
chr6
14131732
14132021
chr3
187957512
187957754
chr6
14133857
14133996
chr3
187957767
187958110
chr6
14135317
14135496
chr3
187958282
187958675
chr6
26020709
26020958
chr3
187958787
187959184
chr6
26032014
26032217
chr3
187959462
187959686
chr6
26045744
26046077
chr3
188299217
188299605
chr6
26056034
26056315
chr3
188471412
188471549
chr6
26056319
26056558
chr3
188471567
188471937
chr6
26123614
26123778
chr4
7728456
7728661
chr6
26123879
26124098
chr4
40198810
40199653
chr6
26124544
26124640
chr4
40199660
40199873
chr6
26124714
26124889
chr4
40199990
40200211
chr6
26156649
26157377
chr4
40200505
40200727
chr6
26158529
26158608
chr4
40200730
40201571
chr6
26158739
26158835
chr4
80327792
80328151
chr6
26197104
26197182
chr4
88011077
88011285
chr6
26197189
26197465
chr4
106157604
106157813
chr6
26216779
26216920
chr4
134727698
134727916
chr6
26217214
26217431
chr4
153249285
153249507
chr6
26234654
26234976
chr4
154624670
154625050
chr6
26250459
26250537
chr4
187509884
187510410
chr6
26250594
26250703
chr4
187557779
187557985
chr6
26252154
26252232
chr4
188924114
188924897
chr6
27100079
27100185
chr5
5182145
5182494
chr6
27100939
27101039
chr5
11110990
11111137
chr6
27101159
27101300
chr5
11236740
11236956
chr6
27114004
27114216
chr5
11364700
11364923
chr6
27114319
27114396
chr5
11397080
11397377
chr6
27114494
27114592
chr5
11411600
11411807
chr6
27277284
27277495
chr5
13864465
13864696
chr6
27777783
27777900
chr5
21783415
21783668
chr6
27777928
27778106
chr5
54964698
54964921
chr6
27782718
27782926
chr6
27799168
27799381
chr6
138201178
138201404
chr6
27833408
27833516
chr6
138202138
138202494
chr6
27834968
27835075
chr6
150954420
150954823
chr6
27839658
27839805
chr6
159238415
159238794
chr6
27860479
27860659
chr7
2963818
2963952
chr6
27860794
27860938
chr7
2963953
2964056
chr6
27861244
27861344
chr7
2969593
2969738
chr6
27861399
27861485
chr7
2976668
2976876
chr6
37138284
37139559
chr7
2977493
2977712
chr6
37140749
37140956
chr7
2978258
2978502
chr6
37141679
37141903
chr7
2979398
2979601
chr6
41903611
41903834
chr7
2983918
2984199
chr6
41904271
41904477
chr7
2985403
2985610
chr6
41904941
41905155
chr7
2987163
2987382
chr6
41908071
41908365
chr7
5569095
5569200
chr6
41909196
41909441
chr7
5569210
5569359
chr6
75965846
75966046
chr7
80285799
80286074
chr6
75969006
75969288
chr7
82387830
82388061
chr6
91004618
91004828
chr7
82453520
82453733
chr6
91005793
91005998
chr7
82763800
82764050
chr6
94120219
94120743
chr7
82784490
82784643
chr6
106534266
106534477
chr7
106508490
106509161
chr6
106536046
106536340
chr7
110545276
110545445
chr6
106543466
106543637
chr7
110697971
110698144
chr6
106547146
106547437
chr7
110737411
110737634
chr6
106552761
106552932
chr7
110746681
110746893
chr6
106552961
106553841
chr7
110762936
110764629
chr6
106554221
106554400
chr7
110764636
110764981
chr6
106554766
106555383
chr7
119915406
119915800
chr6
108040228
108040856
chr7
122634905
122635140
chr6
108041553
108042219
chr7
140453012
140453121
chr6
110777718
110778244
chr7
140453162
140453268
chr6
134491382
134491589
chr7
146997183
146997422
chr6
134491892
134492111
chr7
148506318
148506416
chr6
134492132
134492333
chr7
148506448
148506551
chr6
134492717
134492923
chr7
148508658
148508867
chr6
134493307
134493474
chr7
148513738
148513900
chr6
134493732
134494308
chr7
148523533
148523743
chr6
134494342
134494514
chr7
151943421
151943500
chr6
134494552
134494718
chr8
623880
624090
chr6
134494722
134494795
chr8
3141724
3141942
chr6
134494967
134495974
chr8
4494931
4495105
chr6
138188483
138188650
chr8
8748687
8749284
chr6
138192338
138192683
chr8
8750067
8750281
chr6
138195963
138196172
chr8
18729445
18729937
chr6
138196803
138197021
chr8
75898190
75898400
chr6
138197108
138197313
chr8
101730376
101730457
chr6
138198193
138198407
chr8
103663491
103664160
chr6
138199548
138200525
chr8
104897561
104898479
chr8
113308014
113308283
chr9
21970834
21971023
chr8
113364624
113364791
chr9
21971069
21971170
chr8
113568994
113569205
chr9
21974409
21974881
chr8
116616145
116616886
chr9
21989304
21989976
chr8
122626847
122627163
chr9
21994084
21994405
chr8
128492947
128493338
chr9
22005929
22006067
chr8
128746807
128748893
chr9
22006109
22006187
chr8
128748902
128749969
chr9
22008649
22009012
chr8
128750367
128751183
chr9
24545399
24545922
chr8
128752612
128753235
chr9
24905444
24905729
chr8
128754007
128754731
chr9
27950144
27950532
chr8
128754752
128756424
chr9
37024919
37025642
chr8
128756707
128756931
chr9
37025829
37025996
chr8
128756947
128757361
chr9
37026269
37027015
chr8
128757737
128757921
chr9
37033619
37033797
chr8
128764072
128764292
chr9
37293169
37293378
chr8
128951724
128951896
chr9
37371494
37371879
chr8
130692149
130692503
chr9
37384684
37384911
chr8
130760594
130761023
chr9
37407369
37407588
chr8
131373024
131373443
chr9
78686579
78686854
chr8
136569669
136569842
chr9
139390582
139390950
chr8
136659204
136659414
chr9
139390952
139391172
chr8
137101252
137101464
chr9
139402662
139402868
chr8
137528187
137528570
chr10
5755066
5755273
chr8
138849937
138850149
chr10
89500957
89501139
chr8
139600457
139601255
chr10
89603602
89604077
chr8
139601392
139601569
chr10
89624272
89624350
chr9
5450474
5450616
chr10
89653752
89653825
chr9
5456059
5456200
chr10
89653832
89653909
chr9
5457054
5457446
chr10
89685272
89685379
chr9
5462809
5463160
chr10
89690752
89690894
chr9
5465489
5465622
chr10
89692737
89692810
chr9
5466724
5466867
chr10
89692877
89692951
chr9
5467814
5468022
chr10
89692972
89693037
chr9
5510589
5510804
chr10
89711837
89711966
chr9
5522484
5522636
chr10
89711982
89712058
chr9
5534764
5535047
chr10
89717577
89717714
chr9
5549309
5549627
chr10
89717742
89717811
chr9
5557589
5557762
chr10
89720637
89720904
chr9
5563119
5563251
chr10
90074239
90074419
chr9
5569929
5570140
chr10
90537736
90538027
chr9
13222185
13222409
chr10
90579966
90580319
chr9
16435498
16436307
chr10
90699126
90699647
chr9
19957356
19958178
chr10
90773866
90774076
chr9
20820916
20821095
chr10
91092211
91092423
chr9
20946676
20946849
chr10
91358986
91359298
chr9
21808814
21808891
chr10
131640289
131640505
chr9
21808894
21808973
chr11
58978692
58978791
chr9
21859249
21859469
chr11
58978927
58979095
chr11
58979112
58979365
chr12
49426451
49426592
chr11
65190342
65190557
chr12
49427886
49428116
chr11
65266552
65266924
chr12
49433331
49433507
chr11
65267397
65267603
chr12
49437926
49438391
chr11
65623422
65623506
chr12
49444391
49444595
chr11
69346691
69346940
chr12
49447196
49447491
chr11
102188381
102188945
chr12
57496552
57496735
chr11
111234536
111235068
chr12
57498222
57498396
chr11
111249311
111249530
chr12
57498912
57499150
chr11
111613196
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41572436
chr22
23227897
23228624
chr22
41572800
41573022
chr22
23229332
23229550
chr22
41573300
41573515
chr22
23229562
23229739
chr22
41574255
41574486
chr22
23230012
23231063
chr22
41574685
41574904
chr22
23231072
23231764
chr22
47570209
47570414
chr22
23231927
23232005
chrX
1584324
1585521
chr22
23232062
23232346
chrX
1655789
1656029
chr22
23232362
23232465
chrX
12993264
12993539
chr22
23232517
23232737
chrX
12993544
12994173
chr22
23234612
23235837
chrX
12994289
12994397
chr22
23235847
23236276
chrX
12994444
12994514
chr22
23236277
23236378
chrX
33146106
33146490
chr22
23236387
23236526
chrX
35820576
35821268
chrX
70347816
70348034
chrX
100610984
100611308
chrX
70612661
70612778
chrX
119509280
119509492
chrX
73962123
73963110
chrX
141291052
141291326
chrX
86772953
86773345
chrX
141291357
141291566
chrX
90026453
90026652
chrX
153997383
153997622
(c) obtaining sequencing data from the sequencing library for each of the at least 150,000 evaluable sequencing fragments;
(d) computer processing the sequencing data for each of the at least 150,000 evaluable sequencing fragments to align the sequencing data for each of the at least 150,000 evaluable sequencing fragments to a human reference genome; and
(e) identifying one or more cell-free nucleic acid molecules of the plurality of cell-free nucleic acid molecules, wherein each of the identified one or more cell-free nucleic acid molecules comprises a plurality of phased variants relative to a sequence from the human reference genome, wherein at least 10% of the one or more cell-free nucleic acid molecules comprises a first phased variant of the plurality of phased variants and a second phased variant of the plurality of phased variants that are separated by at least one nucleotide; and
(f) determining a condition of the subject based at least in part on the plurality of phased variants;
wherein an evaluable sequencing fragment is a nucleic acid fragment that covers a region of the genome that comprises two or more predefined mutations from a set of phased variants, wherein the predefined mutations occur within 170 bp of each other in genomic space.