Amniocentesis Genetic Analysis

Diagnostic prenatal testing via WES or WGS on amniotic fluid

14–21 business days (depending on WES vs WGS)Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) on Illumina platformAmniotic fluid (15-20 mL collected via amniocentesis procedure at 15-20 weeks gestation)

What is this test?

Amniocentesis is a diagnostic prenatal procedure performed during pregnancy (typically at 15-20 weeks) where a small sample of amniotic fluid is collected under ultrasound guidance. Unlike NIPT which is a screening test, amniocentesis provides a definitive genetic diagnosis. At IMC Genomics, we analyze the amniotic fluid using either Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) depending on clinical indication and patient preference — offering the most comprehensive prenatal diagnostic capability available.

Key Benefits

Definitive Diagnosis

Unlike screening tests (NIPT), amniocentesis with WES/WGS provides a diagnostic result — confirming or ruling out genetic conditions with high certainty.

Most Comprehensive Prenatal Analysis

WES examines ~20,000 genes; WGS covers the entire genome. This far exceeds traditional karyotype or microarray testing in diagnostic yield.

Detects a Wide Range of Conditions

From chromosomal aneuploidies and microdeletions to single-gene disorders and structural variants — a single test can identify conditions that would otherwise require multiple separate analyses.

Patient Choice: WES or WGS

We offer both WES (faster, focused on protein-coding genes where most known disease variants are found) and WGS (comprehensive, includes non-coding regions and better structural variant detection) — allowing you to choose the approach best suited to your situation.

How It Works

Amniocentesis Procedure

Your obstetrician performs the amniocentesis under continuous ultrasound guidance, collecting 15-20 mL of amniotic fluid. The procedure takes approximately 10-15 minutes.

Cell Culture & DNA Extraction

Fetal cells in the amniotic fluid are cultured to obtain sufficient DNA. Direct extraction from cell-free DNA in the fluid may also be performed for rapid preliminary results.

WES or WGS Sequencing

Based on clinical indication and your preference, DNA undergoes either Whole Exome Sequencing (~20,000 genes) or Whole Genome Sequencing (complete genome) on the Illumina platform.

Comprehensive Analysis

Our bioinformatics pipeline and molecular genetics team analyze the data for chromosomal aneuploidies, copy number variants, single-gene disorders, and structural variants. Variants are classified per ACMG/AMP guidelines.

Results & Genetic Counseling

A comprehensive diagnostic report is provided to your physician. Genetic counseling is included to explain findings, discuss implications, and guide decision-making.

Who should consider this test?

Women with a high-risk NIPT result who need diagnostic confirmation
Women with abnormal ultrasound findings suggesting a genetic condition
Couples with a known family history of a genetic disorder seeking definitive prenatal diagnosis
Women whose serum screening indicates elevated risk for chromosomal or genetic conditions
Couples who want the most comprehensive genetic analysis of their pregnancy

Conditions Screened

All chromosomal aneuploidies (Trisomy 21, 18, 13, sex chromosome abnormalities)Microdeletion and microduplication syndromes (e.g., DiGeorge, Williams, Prader-Willi)Single-gene disorders (cystic fibrosis, SMA, skeletal dysplasias, metabolic conditions)Structural chromosome abnormalities (translocations, inversions)Copy number variants (CNVs) across the genomeNeurodevelopmental and multi-system genetic conditions

Accuracy & Clinical Evidence

Test Accuracy

WES provides >99% diagnostic sensitivity for coding region variants, covering the majority of known disease-causing mutations. WGS offers even broader coverage including non-coding regions, structural variants, and copy number changes.

WES in prenatal diagnosis has been shown to increase diagnostic yield by 8-10% over standard microarray testing in pregnancies with structural anomalies detected on ultrasound. Large studies including the PAGE study and prenatal WES studies demonstrate that exome sequencing identifies clinically significant variants that change management in a meaningful proportion of cases. WGS offers additional detection of non-coding and structural variants.

For Healthcare Providers

Prenatal WES is performed on cultured amniocytes or direct cfDNA with >100x mean coverage of coding regions on the Illumina platform. WGS achieves >30x mean coverage across the complete genome. Analysis includes SNV/indel calling, CNV detection, and structural variant analysis. Trio analysis (fetus + both parents) is strongly recommended to improve variant interpretation. Variants are classified per ACMG/AMP guidelines with additional prenatal-specific considerations. Incidental findings policy follows ACMG secondary findings recommendations with pre-test counseling. Rapid aneuploidy detection (QF-PCR) is available as a 3-day preliminary result.

Important Limitations

Amniocentesis is an invasive procedure carrying a small risk of miscarriage (approximately 0.1-0.3% above background risk).
WES does not cover non-coding regions — for complete genomic analysis, WGS is recommended.
Variants of uncertain significance (VUS) are more common with broader sequencing approaches and may cause uncertainty.
Cell culture for amniocytes may take 7-10 days, adding to total turnaround time.
Not all genetic conditions can be detected — some are caused by mechanisms not captured by sequencing (e.g., imprinting, epigenetic changes).
Maternal cell contamination must be excluded through quality control protocols.