CELL-FREE DNA FOR ASSESSING AND/OR TREATING CANCER

• US 20200131571A1
• Filed: 12/30/2019
• Published: 04/30/2020
• Est. Priority Date: 05/18/2018
• Status: Active Grant

• Current Assignee: Johns Hopkins University
• Original Assignee: Johns Hopkins University
• Inventors: Velculescu, Victor E., Cristiano, Stephen, Leal, Alessandro, Phallen, Jillian A., Fiksel, Jacob, Adleff, Vilmos, Scharpf, Robert B.
• Granted Patent: US 10,982,279 B2
• Time in Patent Office: Days
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G06F 17/18 for evaluating statistical data , e.g. average values, frequency distributions, probability functions, regression analysis forecasting specially adapted for a specific administrative, business or logistic context G06Q10/04
• 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 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/20 Supervised data analysis
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• CPC Class Codes: G16B 50/20 Heterogeneous data integration

Abstract

This document relates to methods and materials for assessed, monitored, and/or treated mammals (e.g., humans) having cancer. For example, methods and materials for identifying a mammal as having cancer (e.g., a localized cancer) are provided. For example, methods and materials for assessing, monitoring, and/or treating a mammal having cancer are provided.

Claims

1-67. -67. (canceled)

68. A method of determining a cell free DNA (cfDNA) fragmentation profile of a mammal, the method comprising:

processing cfDNA fragments obtained from a sample obtained from the mammal into sequencing libraries;

subjecting the sequencing libraries to low-coverage whole genome sequencing to obtain sequenced fragments;

mapping the sequenced fragments to a genome to obtain windows of mapped sequences; and

analyzing the windows of mapped sequences to determine cfDNA fragment lengths.

69. The method of claim 68, wherein the mapped sequences comprise tens or hundreds to thousands of windows.

70. The method of claim 68, wherein the windows are non-overlapping windows.

71. The method of claim 68, wherein the windows each comprises thousands to millions of base pairs.

72. The method of claim 68, wherein a cfDNA fragmentation profile is determined within each window.

73. The method of claim 68, wherein cfDNA fragmentation profile comprises a median fragment size.

74. The method of claim 68, wherein cfDNA fragmentation profile comprises a fragment size distribution.

75. The method of claim 68, wherein the cfDNA fragmentation profile comprises a ratio of small cfDNA fragments to large cfDNA fragments in said windows of mapped sequences.

76. The method of claim 68, wherein the cfDNA fragmentation profile comprises the sequence coverage of small cfDNA fragments in windows across the genome.

77. The method of claim 68, wherein the cfDNA fragmentation profile comprises the sequence coverage of large cfDNA fragments in windows across the genome.

78. The method of claim 68, wherein the cfDNA fragmentation profile comprises the sequence coverage of small and large cfDNA fragments in windows across the genome.

79. The method of claim 68, wherein the cfDNA fragmentation profile is over the whole genome or a subgenomic interval.

96. The method of claim 68, wherein cfDNA fragmentation patterns provide over 20,000 reads per window.

97. The method of claim, 68, wherein genome coverage is from 2×

, 1×

, 0.5×

, 0.2×

or 0.1×

.

80. A method of identifying a mammal as having cancer, the method comprising:

determining a cell free DNA (cfDNA) fragmentation profile in a sample obtained from the mammal; and

identifying the mammal as having cancer when the cfDNA fragmentation profile obtained from the mammal is different from a reference cfDNA fragmentation profile.

81. The method of claim 80, wherein the reference cfDNA fragmentation profile is a cfDNA fragmentation profile of a healthy mammal.

82. The method of claim 80, wherein the reference DNA fragmentation pattern is a reference nucleosome cfDNA fragmentation profile.

83. The method of claim 80, wherein the cfDNA fragmentation profile comprises a median fragment size, and wherein a median fragment size of the cfDNA fragmentation profile is shorter than a median fragment size of the reference cfDNA fragmentation profile.

84. The method of claim 80, wherein the cfDNA fragmentation profile comprises a fragment size distribution, and wherein a fragment size distribution of the cfDNA fragmentation profile differs by at least 10 nucleotides as compared to a fragment size distribution of the reference cfDNA fragmentation profile.

85. The method of claim 80, wherein the cfDNA fragmentation profile comprises a ratio of small cfDNA fragments to large cfDNA fragments in said windows of mapped sequences, wherein a small cfDNA fragment is about 100 base pairs (bp) to 150 bp in length, wherein a large cfDNA fragments is about 151 bp to 220 bp in length, and wherein a correlation of fragment ratios in the cfDNA fragmentation profile is lower than a correlation of fragment ratios of the reference cfDNA fragmentation profile.

86. The method of claim 80, wherein the cfDNA fragmentation profile comprises the sequence coverage of large cfDNA fragments in windows across the whole genome or a subgenomic interval.

87. The method of claim 80, wherein the cfDNA fragmentation profile comprises the sequence coverage of small and/or large cfDNA fragments in windows across the genome or a subgenomic interval.

88. The method of claim 80, wherein the cancer is selected from the group consisting of:

colorectal cancer, lung cancer, breast cancer, gastric cancer, pancreatic cancer, bile duct cancer, and ovarian cancer.

90. The method of claim 80, wherein identifying a mammal with cancer includes a comparison of the cfDNA fragmentation profile with a reference cfDNA fragmentation profile over a subgenomic interval.

91. The method of claim 80, wherein the cancer is treated with or has previously been treated with a treatment comprising administering to the mammal a cancer treatment selected from the group consisting of:

surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, hormone therapy, cytotoxic therapy, immunotherapy, adoptive T cell therapy, targeted therapy, and combinations thereof.

92. The method of claim 80, further comprising identifying one or more cancer-specific sequence alterations or mutations, one or more chromosomal abnormalities, a copy number change in one or more chromosome arms, or identifying one or more aneuploidies in the sample.

93. A method of identifying the tissue of origin of a cancer in a mammal identified as having a cancer, the method comprising:

determining a cell free DNA (cfDNA) fragmentation profile in a sample obtained from the mammal; and

identifying the tissue of origin of the cancer in a mammal when the cfDNA fragmentation profile obtained from the mammal matches a reference cfDNA fragmentation profiles from a mammal identified as having a cancer with the same tissue of origin.

94. The method of claim 93, wherein the reference cfDNA fragmentation profile comprises reference cfDNA fragmentation profiles from mammals identified as having one or more of colorectal cancer, lung cancer, breast cancer, gastric cancer, pancreatic cancer, bile duct cancer, and ovarian cancer.

95. The method of claim 93, wherein the reference DNA fragmentation pattern is a reference nucleosome cfDNA fragmentation profile.

98. A machine learning system for determining a cell free DNA (cfDNA) fragmentation profile of a mammal, the method comprising:

processing cfDNA fragments obtained from a sample obtained from the mammal into sequencing libraries;

subjecting the sequencing libraries to low-coverage whole genome sequencing to obtain sequenced fragments;

mapping the sequenced fragments to a genome to obtain windows of mapped sequences; and

analyzing the windows of mapped sequences to determine cfDNA fragment lengths.