Abstract: Background：Currently in clinical genetic diagnosis, both exome capture sequencing (ES) and whole genome sequencing (WGS) have a wide range of application scenarios. Each has its own advantages in terms of either better costeffective performance or a wider variant detection range. The establishment of an integrative genetic diagnosis process that supports two different library preparation and sequencing protocols is essential to further improve the sensitivity and efficiency of genetic testing. Objective：By integrating the analysis of various variant types fitting both ES and WGS scenarios, the normalization and structuring of complex clinical phenotypes of genetic diseases, and the phenotypeoriented genetic variation analysis system to establish an integrated process from the application of genetic test to the feedback of a diagnostic report. Design：Process development. Methods：An integrated fullprocess closedloop analysis system for highthroughput sequencing data (Fudan Process 3.0) was established including the modules of processing the medical history, extracting structured terms of phenotype, sequencing experiment, detecting variants, interpretating variants, checking quality control, and analyzing both genotypes and phenotypes. In terms of testretest analysis of representative cases, we selected representative cases with various type of conclusive pathogenic variants and diagnosis difficulties to present the analysis process from sequencing experiments and clinical history to the generation of a draft report. Main outcome measures：The structured phenotype terms of patients, the data quality control parameters, the status of variant detection and interpretation, and the final diagnosis during the analysis of representative cases. Results：During the reanalysis of 3 representative cases, the optimized trio genome sequencing, probandonly WGS and CES were carried out respectively. The structured phenotype was successfully extracted from the medical history. The data quality of FastQ and BAM files was well controlled. After interpretation, a combined genotype and phenotype analysis was performed to detect the complex inheritance pattern of three cases respectively. In example 1, detected point mutation NM_058172 (c. 1294C>T and 4q21.22 about 13 kb structural variant deletion on ANTXR2) matched the recessive inheritance model. In example 2, a pathogenic variant m. 14459G>A on mitochondrial gene MTND6 with heterogeneity>99.5% was detected. In example 3, a homozygous pathogenic variant NM_000344（c. 863G>T combined with a single-copy deletion of SMN1 gene）was detected. Conclusion：The Fudan Process 3.0 is well functioned in processing either ES or WGS data to analyze various variant types and draw genetic diagnosis conclusions, especially in handling cases with complex variant types.

Key words: High-throughput sequencing, Exome sequencing, Whole genome sequencing, Integrated pipeline, Genetic diagnosis