Prenatal Diagnosis by Trio Clinical Exome Sequencing: Single Center Experience

Round 1

Reviewer 1 Report

Data are plural (i.e., these data)

"Congenital" literally means "born with" or "present from birth" but all of these fetal anomalies are now diagnosed "before birth" and even before viability. In my opinion the term "fetal anomalies" is preferable to "congenital anomalies"  

Abstract: "20% of spontaneously aborted fetuses" -- unclear. Are these miscarriages, stillbirths, or pregnancy terminations?

Genes have abbreviated names but the text would read better if unnecessary and non-standard abbreviations are minimized (e.g., NT, HME, NS)

Table 1 typo: "classified"

Author Response

Data are plural (i.e., these data).

Corrected thanks

"Congenital" literally means "born with" or "present from birth" but all of these fetal anomalies are now diagnosed "before birth" and even before viability. In my opinion the term "fetal anomalies" is preferable to "congenital anomalies" 

Thank you for pointing out this difference, correction was made in the manuscript.

Abstract: "20% of spontaneously aborted fetuses" -- unclear. Are these miscarriages, stillbirths, or pregnancy terminations? Correction was made. Pag 1 line 14.

Comments on the Quality of English Language

Genes have abbreviated names, but the text would read better if unnecessary and non-standard abbreviations are minimized (e.g., NT, HME, NS).

Done were possible.

Table 1 typo: "classified"

Corrected thanks

Reviewer 2 Report

Cimb-2932134

Prenatal diagnosis by trio clinical exome sequencing: single center experience.

Summary:  The authors examine the use of trio exome sequencing in the diagnosis of abnormalities detected in fetuses where diagnosis by karyotyping and chromosomal microarray sequencing failed.   Samples (n = 51) were obtained from amniotic fluid or the chorionic villus.  The trio CES was effective in diagnosis of 17 to 50 % of the individual anomalies and ~27% of all anomalies examined.

Critique: The description of the project and methodologies are straight forward.  Discussion and conclusions reached are consistent with the presented data.  The paper requires minor editing for grammar (verb tense and plural versus singular).

1.     I would suggest the authors define and discuss clinical exome sequencing in the introduction.

2.     A brief description of DNA isolation procedures should be included.

3.     The first sentence in the results and discussion section needs to be reworded.

4.     Line 105: were all the fetuses male? If so, please state in materials and methods.  What was the sex breakdown of the fetuses?

Recommendations:  Accept after minor revisions.

Please have the article read for English grammar.  In particular, check verb tense, plural versus singular usage.

Author Response

Critique: The description of the project and methodologies are straight forward.  Discussion and conclusions reached are consistent with the presented data.  The paper requires minor editing for grammar (verb tense and plural versus singular).

Corrected thanks

1. I would suggest the authors define and discuss clinical exome sequencing in the introduction. Thank you, new sentence was added in the manuscript. pg 1, and pg 2 line 44-47.
2. A brief description of DNA isolation procedures should be included.

Corrected thanks Pg 2 line 81-84

3. The first sentence in the results and discussion section needs to be reworded.

Corrected thanks

4. Line 105: were all the fetuses male? If so, please state in materials and methods.  What was the sex breakdown of the fetuses?

Thank you, new sentence was added in the manuscript. pg 3, line 117, and in Table 1.

Reviewer 3 Report

The authors describe the results of clinical exome sequencing (CES) in 51 fetuses exibithing ultrasound anomalies between 2018 and 2023. The Non-invasive prenatal testing (NIPT) for trisomy 21, 13 and 18 is NOT mentioned in the manuscript. however it is a highly efficient screening method and has been applied as a first-line or a contingent screening approach all over the world since 2012. The authors have to comment on this.

Page 3: line 96 - 99 and line 115-118 give the same information.

Author Response

Comments and Suggestions for Authors

The authors describe the results of clinical exome sequencing (CES) in 51 fetuses exibithing ultrasound anomalies between 2018 and 2023. The Non-invasive prenatal testing (NIPT) for trisomy 21, 13 and 18 is NOT mentioned in the manuscript. however it is a highly efficient screening method and has been applied as a first-line or a contingent screening approach all over the world since 2012. The authors have to comment on this.

 All fetuses exhibited ultrasound anomalies. Given this, the initial diagnostic approach as today remained invasive procedures, thus, non-invasive prenatal testing (NIPT) was not suggested to the families.

Page 3: line 96 - 99 and line 115-118 give the same information.

Corrected thanks

Reviewer 4 Report

In the manuscript „Prenatal Diagnosis by Trio Clinical Exome Sequencing: Single Center Experience,” the authors reported a trio exome analysis setting (proband and both parents) with a clinical exome sequencing (CES) approach to identify the possible genetic cause after ultrasound anomalies detection. The aim was to evaluate the feasibility of increasing diagnostic yield by trio clinical exome in CMA-negative samples.

The data presented herein are valuable and interesting.

However, some obstacles have to be corrected before the manuscript can be considered for publication.

These include:

2. Materials and Methods

The authors should provide the number of the local ethical committee (Institutional Review Board Statement/Artemisia SPA) approval.

The terms such as HPO should be followed with their full name in parenthesis when mentioned for the first time in the manuscript.

It would be helpful if the authors could briefly explain the method used for DNA isolation or provide the corresponding reference.

3. Results and Discussion

In lines 105-106, the authors have written: “In total, trio clinical exome identified a causative molecular diagnosis (pathogenic variants or likely pathogenic variants) in 12/51 fetus (24%) (Table 2).”

Further in the text, the authors have written: “After excluding fetal aneuploidy, structural defects, and microdeletion/microduplication syndromes, the 18 pregnant women were enrolled in the trio clinical exome sequencing study.” Also, further in the text, the authors have written: “Thirteen fetuses referred with brain malformation were selected for trio clinical exome after excluding fetal aneuploidy, structural defects, and microdeletion/microduplication syndromes.”

However, in the abstract section, the authors have written: “The study revealed pathogenic variants in 24% of the analyzed cases (12 out of 51).”

Thus, to avoid confusion, it would be helpful if the authors could provide an illustrative presentation of the pregnancies covered by the trio exome analysis and reorganize the manuscript text accordingly.

Also, some parts of the manuscript will benefit from English language editing.

A major revision of the manuscript is suggested.

The following sentences should be corrected:

Between January 2018 and October 2023 were admitted at Altamedica Medical Centre 93 (Rome, Italy) 51 pregnant women undergoing to fetal prenatal test after suspected fetal 94 ultrasound investigation (Table 1).

The study was approved by local ethical committee and all participating were provided with written informed consent.

Author Response

2. Materials and Methods

The authors should provide the number of the local ethical committee

Thank you, new sentence was added in the manuscript. pg , line 72-74

The terms such as HPO should be followed with their full name in parenthesis when mentioned for the first time in the manuscript.

Corrected thanks

It would be helpful if the authors could briefly explain the method used for DNA isolation or provide the corresponding reference.

Done thanks

3. Results and Discussion

In lines 105-106, the authors have written: “In total, trio clinical exome identified a causative molecular diagnosis (pathogenic variants or likely pathogenic variants) in 12/51 fetus (24%) (Table 2).”

Further in the text, the authors have written: “After excluding fetal aneuploidy, structural defects, and microdeletion/microduplication syndromes, the 18 pregnant women were enrolled in the trio clinical exome sequencing study.” Also, further in the text, the authors have written: “Thirteen fetuses referred with brain malformation were selected for trio clinical exome after excluding fetal aneuploidy, structural defects, and microdeletion/microduplication syndromes.”

However, in the abstract section, the authors have written: “The study revealed pathogenic variants in 24% of the analyzed cases (12 out of 51).”

Thus, to avoid confusion, it would be helpful if the authors could provide an illustrative presentation of the pregnancies covered by the trio exome analysis and reorganize the manuscript text accordingly.

Thank you for pointing out these difficulties, correction was made by adding a consort diagram (Figure1).

Also, some parts of the manuscript will benefit from English language editing.

A major revision of the manuscript is suggested.

Comments on the Quality of English Language

The following sentences should be corrected:

Between January 2018 and October 2023 were admitted at Altamedica Medical Centre 93 (Rome, Italy) 51 pregnant women undergoing to fetal prenatal test after suspected fetal 94 ultrasound investigation (Table 1).

The study was approved by local ethical committee and all participating were provided with written informed consent.

Corrected thanks