A method of enriching a target nucleotide sequence having a locus of interest from a nucleic acid sample comprising a double-stranded nucleic acid template comprising the target nucleotide sequence, the method comprising: (a) ligating a universal adaptor to the double-stranded nucleic acid template to provide a ligated nucleic acid, wherein the universal adaptor is an oligonucleotide comprising a duplex portion at a first end and a non-duplex portion at a second end, and wherein the double-stranded nucleic acid template is ligated to the universal adaptor via the first end, both ends of the double-stranded nucleic acid template are ligated to the universal adaptor, and wherein a first strand of the non-duplex portion comprises a molecular barcode comprising degenerately designed nucleobases, and the duplex portion of the universal adaptor comprises a sample barcode; (b) dissociating the ligated nucleic acid into a first strand and a second strand, wherein the first strand comprises the target nucleotide sequence; (c) annealing an outside primer to 3' portion of the first strand of the ligated nucleic acid in the vicinity of the target nucleotide sequence; (d) extending the outside primer over the full length of the first strand of the ligated nucleic acid using a DNA polymerase to provide a nascent DNA linear amplification duplex; (e) dissociating the nascent DNA linear amplification duplex at a sufficiently high temperature into the first strand of the ligated nucleic acid and a single-stranded DNA linear amplification product; (f) repeating steps (c)-(e) for one or more DNA linear amplification cycles; (g) contacting the single-stranded DNA linear amplification products with a DNA polymerase, a universal adaptor primer and an inside primer under a condition sufficient for PCR amplification of the target nucleotide sequence, wherein the universal adaptor primer anneals to a complementary sequence of the non-duplex portion of the universal adaptor in the single-stranded DNA linear amplification products, wherein the inside primer comprises a sequence at the 3' end that specifically anneals to the target nucleotide sequence, and wherein the inside primer is nested with respect to the outside primer for the locus of interest; and (h) repeating step (g) for one or more cycles of PCR amplification to provide amplicons of the target nucleotide sequence, thereby enriching the target nucleotide sequence; the inside primer and outside primer hybridize specifically to a same strand of the target nucleotide, and a hybridization site of the outside primer is farther away from the locus of interest than a hybridization site of the inside primer; and the hybridization site of the outside primer is closer to the 3' end of the target nucleotide sequence than the hybridization site of the inside primer. (a) ligating a universal adaptor to the double-stranded nucleic acid template to provide a ligated nucleic acid, wherein the universal adaptor is an oligonucleotide comprising a duplex portion at a first end and a non-duplex portion at a second end, and wherein the double-stranded nucleic acid template is ligated to the universal adaptor via the first end, both ends of the double-stranded nucleic acid template are ligated to the universal adaptor, and wherein a first strand of the non-duplex portion comprises a molecular barcode comprising degenerately designed nucleobases, and the duplex portion of the universal adaptor comprises a sample barcode; (b) dissociating the ligated nucleic acid into a first strand and a second strand, wherein the first strand comprises the target nucleotide sequence; (c) annealing an outside primer to 3' portion of the first strand of the ligated nucleic acid in the vicinity of the target nucleotide sequence; (d) extending the outside primer over the full length of the first strand of the ligated nucleic acid using a DNA polymerase to provide a nascent DNA linear amplification duplex; (e) dissociating the nascent DNA linear amplification duplex at a sufficiently high temperature into the first strand of the ligated nucleic acid and a single-stranded DNA linear amplification product; (f) repeating steps (c)-(e) for one or more DNA linear amplification cycles; (g) contacting the single-stranded DNA linear amplification products with a DNA polymerase, a universal adaptor primer and an inside primer under a condition sufficient for PCR amplification of the target nucleotide sequence, wherein the universal adaptor primer anneals to a complementary sequence of the non-duplex portion of the universal adaptor in the single-stranded DNA linear amplification products, wherein the inside primer comprises a sequence at the 3' end that specifically anneals to the target nucleotide sequence, and wherein the inside primer is nested with respect to the outside primer for the locus of interest; and (h) repeating step (g) for one or more cycles of PCR amplification to provide amplicons of the target nucleotide sequence, thereby enriching the target nucleotide sequence;