WES (including CES)

1. Clinical indications

Family with a history genetic disease

Patients with atypical disease characteristics without diagnosis

Patients with physical and mental disabilities

Couples who want to check the reason of recurrent miscarriage or stillbirth

Patients who have failed to find a genetic cause by clinical exome sequencing

2. Technology

Wet lab(Genomic DNA)

Illumina NovaSeq 6000; Capture based tech (IDT / Agilent probe)

Average 100X sequencing coverage, Q30 > 90%, 20X coverage rate > 95%

* For CES, gene panel covers 5,642 genes associated with known autosomal recessive, autosomal dominant and X-linked diseases listed in the Online Mendelian Inheritance in Men (OMIM) catalogue


Detects SNVS, InDels(below<50dp) and CNVs (above>50 bp) in the exome

Dry lab (Bioinformatics)

VeritaTrekker® Variants Detection System (SNVs, CNVs, SVs)

Enliven® Data Annotation System

Cruxome Interface

3. Case sharing

Two female siblings originally diagnosed with “cerebral palsy” had received long-term treatment with no significant improvement in perennial paralysis and language skills. Family WES tests found that both girls inherited pathogenic mutations in the GCH1 gene associated with the metabolic disease Dopa-responsive dystonia (DRD). Both girls have now been successfully effectively treated by oral Medopa (Benserazide-Levodopa), reducing the severity of symptoms and improving their quality of life. This case fully demonstrates the important role of WES in the precise diagnosis and treatment of genetic diseases.

4. Why use BerryGenomics for WES?

Integrated professional teams for sequencing, data analysis and reporting

Fast turnaround time

Comprehensive disease report for clinical geneticist, including supplementary file listing all potentially pathogenic mutations

Option of uploading raw data by Cloud to local hospitals for secure storage and reanalysis options

Competitive pricing

5. The clinical significance of WES/CES

Can provide a precise diagnosis for children with unexplained phenotypes where previous testing has failed to give the answer

Can help explain the genetic basis of fetal structural abnormalities detected by ultrasound during pregnancy

Can point the way to potential treatment options for children to improve their health and quality of life

Can guide the development of prenatal and preimplantation genetic tests so couples

can confidently proceed to have a second child free of the familial disease condition


1. Clinical indications


Children or adults with unexplained disease symptoms (Peripheral blood DNA)


Miscarriage products of conceptions (chorionic villus DNA)

Fetal ultrasound structural abnormalities (amniocyte DNA)

High risk pregnancies (advanced maternal age, soft ultrasound marker)

2. Technology

Wet lab

Patent PCR-free library construction technology

Low input: 10-50ng DNA

Detection of aneuploidy, large fragment deletion/duplication, whole genome CNVs (>100kb), chromosome mosaicism (>10%)

Dry lab (Bioinformatics)

CNV analysis system

3. Case sharing – apoblema testing

Clinical information:

31 yrs, induced labor one time, a biochemical pregnancy, six times of embryo arrest. She did such test at 7+3 weeks, no fetal buds or fetal heart.

Test results:

seq [hg19] dup(2)(q36.1q37.3)
chr2:g. 224740001_­243020000dup

seq [hg19] del(8)(q24.23q24.3)
chr8:g. 138800001_146300000del

Follow up FISH verified that the husband had t(2;8)(q36.1;q24.23) balanced translocation. The couple choose PGT and they successfully achieved a healthy baby.

CNV-seq identified terminal deletion/duplication events at the end of chromosomes 2 and 8, indicating an balanced translocation.

4. Why use BerryGenomics? (Advantage)

Low cost

Integrated professional teams for sequencing, data analysis and reporting

Fast turnaround time

Reliable and accurate results equivalent to current array CGH and SNP arrays

5. The significance of CNV-Seq

Can detect aneuploidy, CNVs (resolution 0.1Mb) and mosaicism (resolution) that are associated with known chromosome disease syndromes

Applicable to genetic diagnosis of preconception, prenatal and postnatal samples

Can identify a genetic cause of miscarriage samples

Reliable results can be obtained from rare samples or samples with low amounts of DNA


1. Introduction

Comprehensive and rapid transcriptome sequencing for human, animals and plants samples under a certain tissue or cell states. FOR RESEARCH ONLY.

Sample type: dsDNA generated from polyA+ mRNA

2. Technology

Illumina NovaSeq 6000

Validated sequencing pipeline

More accurate detection of gene expression changes

No need to design new probes for known sequences, saving time and cost

3. Case sharing – Arabidopsis blue light receptor protein

RNA-Seq helps demonstrate the photo-induced protein dimerization of plant cryptochromes is a key step in their primary photoreaction.

^Qin Wang, Zecheng Zuo, Chentao Lin, et al., Photoactivation and inactivation of Arabidopsis cryptochrome 2. PLANT PHOTOBIOLOGY.(2016),VOL 354 ISSUE 6310.

WGS (Human)

1. Introduction

Offers genome wide detection of DNA variants including SNP, CNV, Indel and SV

Ability to detect rare and novel (de novo) genetic variants

Applicable to patients whose WES has failed to detect pathogenic variants

Sample type: Genomic DNA

2. Technology

Wet lab

NovaSeq 6000

Average sequencing depth ≥30X

Dry lab (Bioinformatics)

Berry own database (0ver 400,000 cases)

3. Case sharing – gastric cancer-related genetic variation information

Gastric cancer is a heterogeneous disease with different molecular etiologies. We performed WGS of 100 pairs of tumor-normal samples at an average effective sequencing depth of 84X. Bioinformatics analysis identified tumour-specific somatic mutations in known genes such as TP53, ARID1A, CDH1 and in a newly discovered gene MUC6. Mutations in driver genes were also found including CTNNA2, GLI3, and RNF43. The study also revealed that that 4.3% of RHOA mutations in diffuse tumors were closely related to the most common interference pathways (adhesion links and focal adhesions) in gastric cancer.

4. Why use BerryGenomics?

Output as high as 200,000 Gb raw data per week

Integrated professional teams for sequencing, data analysis and reporting

Fast TAT to report of 25 days

Comprehensive disease report for clinical geneticist, including supplementary file listing all potentially pathogenic mutations

Option of uploading raw data by Cloud to local hospitals for storage and reanalysis

Kai Wang, Siu Tsan Yuen, et al., Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nature Genetics. (2014),doi:10.1038/ng.2983.

WGS (Animal or Plant)

1. Introduction

The genome-wide sequencing of animals and plants genomes is important is understand differences in species and varieties. The information can be used for population genetic polymorphism analysis, evolutionary analysis, identification of new functional genes, breeding guidance and genetic modifications.

2. Technology

NovaSeq 6000

Obtain information on CDS, introns, intergenic regions

SNP, CNV, InDel, SV and other variation information

Structural variations and genomic CNVs in large fragments

3. Case sharing – Genome-wide resequencing for Soybean

Identification of domesticated and improved genes in the soybean genome is important for guiding soybean breeding. Three types of germplasm lines were selected in this study. A total of 302 representative soybean germplasm resources were sequenced at a depth was greater than 11X. The results showed that the genetic polymorphism of soybean was significantly reduced during acclimation and improvement. Genome-wide association analysis on seed size, seed coat color, growth habit, oil content and other traits identified a series of significant associated genetic sites.

Zhou Z, Jiang Y, et al., Resequencing 302 wild and cultivated accessions genes related to domestication and improvement in soybean. Nat Biotechnol.(2015),doi:10.1038/nbt.3096.

The decline of linkage imbalance (LD) in GWAS analysis of soybean genomic population