Background Massively parallel sequencing of circulating cell-free fetal DNA from matemal plasma has been applied widely to fetal chromosome aneuploidies identification.Non-invasive prenatal testing (NIPT) mainly focused on chromosome for prenatal screening in second-trimester recently.The biochemical and biophysical markers combined with normalized chromosome representation (NCR) and GC-content correction algorithms, would permit one to discover the genome contents variation of each chromosome earlier and more comprehensive.For prenatal diagnose of clinical samples, the timeliness and comprehensive of data analysis for each chromosome might be substitute partly invasive prenatal testing via application of those approaches.Therefore, we explored the operational necessities for fetal chromosome abnormal using comprehensive manners.Methods Enrolled 595 pregnant women who undergoing diagnose protocol and have invasive karyotype procedures, corresponding to 49 trisomy 21, 14 trisomy 18, 1trisomy 13, 5 monosomy X and 1 deletion syndrome in second-trimester (15-20 weeks) , 2 trisomy 21, 2 trisomy 16, 1 trisomy 13, 1 trisomy 15, 1 trisomy 2 and 1 monosomy X in first-trimester (7-13 weeks).We sequenced the plasma cell-free fetal DNA extracted from these samples at low coverage.For each chromosome of each sample, the normalized chromosome representation (NCR) for GC-passed value and z-score were calculated.The sequencing classifications were compared with fetal karyotypes from invasive procedures.Results Within a cohort of 575 samples that were divided into three classifications.In total, seventy-eight samples containing a fetal chromosome aneuploidy, trisomy 21, trisomy 18, trisomy 13 and 45, XO were accurately identified with a detection sensitivity and specificity of 100% and 99.83% in first-trimester (7-13 weeks) and second-trimester (15-20 weeks).Meanwhile, six first-trimester screening or rare autosomal aneuploidy specimens (7-13 weeks) were detected in which the karyotype was trisomy 2, 13, 15 and 45, XO.At last, we discussed one sample that the karyotype and genotype for chromosome 18 short arm deletion were certified by amniocentesis and SNP microarray, it showed that the sequence had uneven distribution of chromosome 18.Conclusions NIPT can detect nearly all cases of Down syndrome, trisomy 18, trisomy 13, monosomy X, rare chromosomal aneuploidies and deletion syndrome at a low false-positive rate in first-trimester (7-13 weeks) and second-trimester (15-20 weeks) using comprehensive clinical parameters.Meanwhile, we researched the possible primary source of free fetal DNA for the first time based on NIPT.