Detecting chromosomal aberrations associated with cancer using genomic sequencing

A method for analyzing a biological sample from a subject for a chromosomal aberration associated with a tumor in the subject, the method comprising:

• (a) analyzing a plurality of cell-free nucleic acid molecules from the biological sample of the subject, wherein analyzing the plurality of cell-free nucleic acid molecules comprises:
• i. sequencing the plurality of cell-free nucleic acid molecules from the biological sample of the subject, thereby obtaining a plurality of sequenced tags from the sequencing of the plurality of cell-free nucleic acid molecules, wherein a given sequenced tag of the plurality of sequenced tags corresponds to at least one end of a given cell-free nucleic acid molecule of the plurality of cell-free nucleic acid molecules, wherein the sequencing comprises obtaining at least 120,000 sequenced tags;
• and
• ii. obtaining a plurality of chromosomal locations by aligning, using a computer system, the plurality of sequenced tags to a reference genome, wherein a given chromosomal location of the plurality of chromosomal locations corresponds to the at least one end of the given cell-free nucleic acid molecule;
• (b) generating a parameter of a relative amount between (i) a first number of sequenced tags of the plurality of sequenced tags aligning to a first chromosomal location of the plurality of chromosomal locations in the reference genome, and (ii) a second number of sequenced tags of the plurality of sequenced tags aligning to one or more second chromosomal locations in the reference genome;
• and
• (c) determining a classification of whether the first chromosomal location exhibits the chromosomal aberration associated with the tumor in the subject by processing the parameter against one or more cutoff values, the chromosomal aberration in the biological sample being an amplification or a deletion of a sequence at the first chromosomal location in the reference genome.