Pregnancy and Antenatal Genomics

Types of chromosomal abnormalities

Frequency and the Types of chromosomal abnormalities in patients with Primary Amenorrhea in Sudan

Hiba Satti ,Imad Fadl-Elmula , Lamis Beshir , Abdelbagi Alzain

Study objective: to detect the frequency and the type of chromosomal abnormalities  in patients with primary Amenorrhea (PA)

Material and Methods:Chromosomal analysis  was carried out for  patients with primary amenorrhea who attended Elite genetics center or referred from other clinics in Khartoum, Sudan were retrospectively analyzed from 2017and 2018.

Results:The present study aimed at performing chromosomal analysis in patients presenting with primary amenorrhea (n=169) employing G banding. The karyotype results revealed that 50.3% (n=85) of the patients had normal karyotypes consistent with their female sex. 49.7% (n=84) showed abnormal karyotypes. Karyotype abnormalities were due to numerical aberration, structural abnormalities in the chromosomes or XY karyotypes inconsistent with the patients’ sex. 
Conclusion : Chromosomal abnormalities are common causes of primary amenorrhea in Sudanese patients. The results of the present study imply the inclusion of chromosomal analysis and genetic counseling for all patients with PA for early diagnosis. Of 169 cases with PA, 85 patients had normal karyotypes which suggest that other causes at gene level need to be further explored beside chromosomal abnormalities.
primary amenorrhea(PA), chromosomal abnormalities, karyotyping, cytogenetic study,
turner syndrome, testicular feminization syndrome, triple X karyotype






Sarah Ahmed Abstract



Sarah I Y Ahmed

Institute of Endemic Diseases, University of Khartoum


Background: Adaptive genes to low oxygen in the high altitudes of Chinese Tibet, African Ethiopian plateau, and the Andeas of America can also be protective in diseases like preeclampsia, which may result from deregulation of hypoxia pathway.

Aim: To study the genetic variants of high altitude adaptive genes in the samples of preeclampsia in compare to normal pregnancy controls as signs of acclimatization and adaptation.

Methods: Using computational tools, a total of 36 RNA-seq samples from the amniotic fluid, were retrieved from NCBI; 19 pre-eclamptic samples and 17 full-term birth samples. Variant calling pipeline was performed for the raw RNA-seq reads. FASTQ files were downloaded from the database and were aligned to the human genome build GRCh37/hg19 to identify both known and novel SNPs and indels. Results: Adaptive variants of genes that were found predominately in highlanders were also found both in normal hypoxia of pregnancy (N=52.9%) and in pathological condition of preeclampsia with no significant difference. Interestingly, higher adaptive alleles frequency were found in normal controls of pregnancy compared to cases of Preeclampsia, p value = 0.003. The mean homozygous genotype frequency for adaptive variants were even much higher in controls than in cases, P value = 0.0001. Conclusion: The high homozygosity in the controls indicates the higher ability of controls to retain beneficial variants, which can ultimately drives the natural selection of variants towards fitness, while the heterozygosity of cases reflects the higher genetic variability that associates with slow fixation rate to the adaptive variants, which results in insufficient adaptation of spiral arterioles and shallow trophoblastic invasion, resulting in reduced uteroplacental blood flow leading to placental hypoxia, which is believed to be the underlying cause of Preeclampsia.