A method of analyzing a biological sample of an organism for chromosomal deletions or amplifications associated with cancer, the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer, wherein at least some of the nucleic acid molecules are cell-free in the biological sample, the method comprising: determining first and second haplotypes for normal cells of the organism at a first chromosomal region, the first chromosomal region including a first plurality of loci, wherein the first and second haplotypes are heterozygous at each of the first plurality of loci; for each of a plurality of the nucleic acid molecules in the biological sample: identifying a location of the nucleic acid molecule in a reference genome of the organism; and determining a respective allele of the nucleic acid molecule; identifying a first group of nucleic acid molecules as being from the first haplotype based on the identified locations and determined alleles, the first group including at least one nucleic acid molecule located at each of the first plurality of loci; identifying a second group of nucleic acid molecules as being from the second haplotype based on the identified locations and determined alleles, the second group including at least one nucleic acid molecule located at each of the first plurality of loci; calculating, with a computer system, a first value of the first group of nucleic acid molecules, the first value defining a property of the nucleic acid molecules of the first group; calculating, with the computer system, a second value of the second group of nucleic acid molecules, the second value defining a property of the nucleic acid molecules of the second group; and comparing the first value to the second value to determine a classification of whether the first chromosomal region exhibits a deletion or an amplification in any cells associated with cancer. determining first and second haplotypes for normal cells of the organism at a first chromosomal region, the first chromosomal region including a first plurality of loci, wherein the first and second haplotypes are heterozygous at each of the first plurality of loci; for each of a plurality of the nucleic acid molecules in the biological sample: identifying a location of the nucleic acid molecule in a reference genome of the organism; and determining a respective allele of the nucleic acid molecule; identifying a first group of nucleic acid molecules as being from the first haplotype based on the identified locations and determined alleles, the first group including at least one nucleic acid molecule located at each of the first plurality of loci; identifying a second group of nucleic acid molecules as being from the second haplotype based on the identified locations and determined alleles, the second group including at least one nucleic acid molecule located at each of the first plurality of loci; calculating, with a computer system, a first value of the first group of nucleic acid molecules, the first value defining a property of the nucleic acid molecules of the first group; calculating, with the computer system, a second value of the second group of nucleic acid molecules, the second value defining a property of the nucleic acid molecules of the second group; and comparing the first value to the second value to determine a classification of whether the first chromosomal region exhibits a deletion or an amplification in any cells associated with cancer. identifying a location of the nucleic acid molecule in a reference genome of the organism; and determining a respective allele of the nucleic acid molecule; identifying a first group of nucleic acid molecules as being from the first haplotype based on the identified locations and determined alleles, the first group including at least one nucleic acid molecule located at each of the first plurality of loci; identifying a second group of nucleic acid molecules as being from the second haplotype based on the identified locations and determined alleles, the second group including at least one nucleic acid molecule located at each of the first plurality of loci; calculating, with a computer system, a first value of the first group of nucleic acid molecules, the first value defining a property of the nucleic acid molecules of the first group; calculating, with the computer system, a second value of the second group of nucleic acid molecules, the second value defining a property of the nucleic acid molecules of the second group; and comparing the first value to the second value to determine a classification of whether the first chromosomal region exhibits a deletion or an amplification in any cells associated with cancer.