[esha dalal]

Hello everyone, 

I need comment regarding karyotype of a 27 yrs old female patient. 

There is a light band on chromosome 3p.

Please comment on how to interpret this. 

Thanks in advance. 

[Güven Toksoy]

Dear Esha,

 first of all, the reason why the patient is referred for genetic testing is important, so, I suggest you share the indication info.  Another issue is that the resolution of the band and karyogram are low.  Therefore, I recommend repeating the study to obtain a longer resolution and more sharply banded chromosomes. If the indication leads to a balanced expectation of a chromosomal abnormality, an array study will not be useful. in some karyograms, the presence of satellites at 3p can be suspected, you can try NOR banding to confirm this. If NOR is negative, 3p subtelomeric FISH and 3 painting FISH may be informative. 

If the patient has clinical findings suggestive of an unbalanced chromosomal abnormality, I would recommend an array study or CNV analysis with NGS.

regards

Doç. Dr. Güven Toksoy

Tıbbi Genetik AD

İstanbul Tıp Fakültesi

İstanbul Üniversitesi

Assoc Prof.Dr. Güven Toksoy (PhD)

Dep.artment of Medical Genetics

Istanbul Faculty of Medicine

İstanbul Universty

+90 212 4142000/35034

tok...@gmail.com.

guven....@istanbul.edu.tr

esha dalal <esha...@gmail.com>, 14 Eki 2024 Pzt, 09:39 tarihinde şunu yazdı:

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[Cleide Borovik]

First, What is the clinical reason for asking for a Karyotype? Second, look at chromosome 15 satellites. Could be a translocation 3;15?

Cleide

--

[EVANGELIDOU Paola]

Hello,

 

Thank you for sharing these karyotypes. What is the reason for referral of this patient?

The resolution of the chromosomes is not very good, therefore I cannot tell for sure if we are talking about a “light band” as you say or a pericentric inversion. Also the rest of the chromosomes are difficult to analyse due to the resolution, therefore the possibility of reciprocal translocation cannot be ruled out. I would suggest further investigation with C- banding, FISH etc to resolve this.

 

Kind regards,

 

Paola

 

Paola Evangelidou, PhD
Scientist | Cytogenetics and Genomics Department
Academic Staff | The Cyprus Institute of Neurology & Genetics
6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus | PO Box 23462, 1683, Nicosia, Cyprus
: +357 - 22 358600 (Switchboard) | : +357 - 22 392726 (Direct Line) | Fax: +357 22 392793 | : pa...@cing.ac.cy | : https://www.cing.ac.cy

  

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From: cytogenetics-methods...@googlegroups.com <cytogenetics-methods...@googlegroups.com> On Behalf Of esha dalal
Sent: 10 October 2024 16:16
To: cytogenetics-methods...@googlegroups.com
Subject:

 

Caution: This email did not come from CING. If you do not know the sender, do not click on any links, or attachments, or respond.

 

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[Mustafa Acar]

I thought it resembled a satellite. If you do NOR staining, it might help. Ectopic NOR has been reported on other non-acrocentric chromosomes.

(PMID: 10227407)

14 Ekim 2024 Pazartesi tarihinde saat 09:39:15 UTC+3 itibarıyla esha dalal şunları yazdı:

[Istok828]

Hello, this is definitely an inversion.

четверг, 17 октября 2024 г. в 05:01:16 UTC-5, Mustafa Acar:

[Jasen Anderson]

What are the clinical indications? Infertility or other phenotype? 

There's a number of things you can try. Whole paint 3 and also centromere chromosome 3 to exclude inversion first, the constriction is curious as is the p-terminus, looks a bit like satellites.

If not inversion from the centromere point of view, try NOR staining or Acro-p probe ( https://metasystems-probes.com/en/probes/xl/d-5440-050-or/ ) to see if that's satellites at the top,  If it isn't centromere 3 at the constriction,  it could be a Neocentromere. Just my initial thoughts. The abnormal chromosome looks bigger too, microarray would be a useful second round of testing to exclude extra material. 

Cheers

Jasen 

--

[esha dalal]

Thank you all for your valuable suggestions.
The AMH level is very low (0.528 ng/ml) which is very low.

So before starting IVF cycle karyotype is recommended.

--

You received this message because you are subscribed to the Google Groups "Cytogenetics methods and trouble-shooting Forum" group.
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[Jasen Anderson]

Ok so likely unaffected phenotype apart from possible fertility issues. Keep us posted as to what steps you take to investigate and the outcome. 

Cheers

Jasen

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDQYfawZsdm0nceT58efQ8aXeguiow8pxCHP%2Bs95v0uusA%40mail.gmail.com.

[esha dalal]

Sure

Thank you so much for your guidance.

Once again thank you so much to all

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CADEgMMC%3D%3DUMHP--Xx5zfofcTB9sjgXJ3r_2Tnh3oRJcqZbzzkg%40mail.gmail.com.

[esha dalal]

Hello everyone, 

Can anyone please suggest Whole Exome Sequencing (WES) will be helpful in this case? 

Thanks in advance... 

Esha

[Jasen Anderson]

I'd just go microarray first.. Cheaper. See what results are. 

Cheers

Jasen

To view this discussion visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDS00EttpiqQ1Fko%3DAxbzAy_JLt7iWjNLRmk9YgLbm_DzA%40mail.gmail.com.

[esha dalal]

Sir, CMA is done and it's normal. 

So, I was thinking to do WES or can suggest PGT on embryo if patient choose IVF. 

And if patient wish for a natural pregnancy (as young age 27 yrs) , NIPT should be suggested in 1st trimester? 

Thanks

Esha

To view this discussion visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CADEgMMA326BxaB69-Q%2BsVo3zdpuN56NSELTtm3gKVsJpnhO_DA%40mail.gmail.com.

[Jasen Anderson]

Hi. I'm not familiar with what extra information WES will provide in relation to the initial finding, if any, but as microarray did not detect anything, it would suggest that there's likely no consequences on a phenotype in any offspring that carry it. Did you attempt NOR banding or other techniques to exclude satellites from acrocentric chromosomes? Whole paint FISH? 

Cheers

Jasen

To view this discussion visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDTKjQi9PA_Qsvj3NRnf-t8Cwb_JKBTSDjqPf9LdM2SpKQ%40mail.gmail.com.

[David Zhang]

Hi Esha

I agree with others' opinion that this is very likely a pericentric inversion. Personally I would try a higher resolution karyotype (>550 bphs) or metaphase FISH (with chr3 cen probe) in the first place, or go OGM or long range sequencing for more advanced platform on structural variation.

Since CMA returned a balanced result, I would not suggest further tests targeting CNV. 

BTW: WES is not very reliable on CNV detection because of the low genomic coverage. If one must use NGS platform on CNV, WGS would be a better choice. But its not very cost effective.

Cheers

David

[esha dalal]

Hello David, 

Thank you so much for your valuable suggestions. 

Will try for the high resolution karyotype. 

Once again I would like to thank everyone. 

Esha

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[Alka Anilkumar]

Hello All

Check for NOR banding to rule out the presence of satellite, after confirmation go ahead with advanced techniques.

With Best Regards

Dr Alka Anilkumar

Forwarded Conversation
Subject:
------------------------

From: esha dalal <esha...@gmail.com>
Date: Mon, Oct 14, 2024 at 12:09 PM
To: <cytogenetics-methods...@googlegroups.com>

Hello everyone, 

I need comment regarding karyotype of a 27 yrs old female patient. 

There is a light band on chromosome 3p.

Please comment on how to interpret this. 

Thanks in advance. 

--

You received this message because you are subscribed to the Google Groups "Cytogenetics methods and trouble-shooting Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytogenetics-methods-and-t...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDT_PrmbhMmcufRUZ8Oh8XUzPB_SsvnZLz9YdP2rB-EDpg%40mail.gmail.com.

----------
From: Güven Toksoy <tok...@gmail.com>
Date: Thu, Oct 17, 2024 at 3:29 PM
To: <cytogenetics-methods...@googlegroups.com>

Dear Esha,

 first of all, the reason why the patient is referred for genetic testing is important, so, I suggest you share the indication info.  Another issue is that the resolution of the band and karyogram are low.  Therefore, I recommend repeating the study to obtain a longer resolution and more sharply banded chromosomes. If the indication leads to a balanced expectation of a chromosomal abnormality, an array study will not be useful. in some karyograms, the presence of satellites at 3p can be suspected, you can try NOR banding to confirm this. If NOR is negative, 3p subtelomeric FISH and 3 painting FISH may be informative. 

If the patient has clinical findings suggestive of an unbalanced chromosomal abnormality, I would recommend an array study or CNV analysis with NGS.

regards

Doç. Dr. Güven Toksoy

Tıbbi Genetik AD

İstanbul Tıp Fakültesi

İstanbul Üniversitesi

Assoc Prof.Dr. Güven Toksoy (PhD)

Dep.artment of Medical Genetics

Istanbul Faculty of Medicine

İstanbul Universty

+90 212 4142000/35034

tok...@gmail.com.

guven....@istanbul.edu.tr

esha dalal <esha...@gmail.com>, 14 Eki 2024 Pzt, 09:39 tarihinde şunu yazdı:

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAHK63ijV_Otz3j%2BoTAxKqtnQCW8SuQtSadyPp1RY3UFXhHg0AA%40mail.gmail.com.

----------
From: Cleide Borovik <cleide....@gmail.com>
Date: Thu, Oct 17, 2024 at 3:30 PM
To: <cytogenetics-methods...@googlegroups.com>

First, What is the clinical reason for asking for a Karyotype? Second, look at chromosome 15 satellites. Could be a translocation 3;15?

Cleide

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CANSikuB-wNE3vUBmc0zZRt1j9e9KPTyPdFcbTw5_3bx%2B72RdyA%40mail.gmail.com.

----------
From: 'EVANGELIDOU Paola' via Cytogenetics methods and trouble-shooting Forum <cytogenetics-methods...@googlegroups.com>
Date: Thu, Oct 17, 2024 at 3:30 PM
To: cytogenetics-methods...@googlegroups.com <cytogenetics-methods...@googlegroups.com>

Hello,

 

Thank you for sharing these karyotypes. What is the reason for referral of this patient?

The resolution of the chromosomes is not very good, therefore I cannot tell for sure if we are talking about a “light band” as you say or a pericentric inversion. Also the rest of the chromosomes are difficult to analyse due to the resolution, therefore the possibility of reciprocal translocation cannot be ruled out. I would suggest further investigation with C- banding, FISH etc to resolve this.

 

Kind regards,

 

Paola

 

Paola Evangelidou, PhD
Scientist | Cytogenetics and Genomics Department
Academic Staff | The Cyprus Institute of Neurology & Genetics
6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus | PO Box 23462, 1683, Nicosia, Cyprus
: +357 - 22 358600 (Switchboard) | : +357 - 22 392726 (Direct Line) | Fax: +357 22 392793 | : pa...@cing.ac.cy | : https://www.cing.ac.cy

  

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The contents of this email and any attachments are confidential. They are intended for the attention of the named recipient(s) only. If you have received this email in error, please notify the sender immediately and do not disclose the contents to anyone or make copies thereof. Any disclosure, publication, copying, retransmission, distribution or other use of, or taking any action in reliance upon, this e-mail or its attachments by non-authorised persons is strictly prohibited. The CING processes personal data in accordance with the General Data Protection Regulation (EU) 2016/679 (GDPR) and the national legislation, Law 125(I)/2018. Please refer to our Privacy Policy ( https://www.cing.ac.cy/en/privacypolicies ).

This email has been scanned internally by CING systems for viruses, vandals, and malicious content. The CING accepts no liability for any damage caused by any virus transmitted by this email.
please consider your environmental responsibility before you print this email.

From: cytogenetics-methods...@googlegroups.com <cytogenetics-methods...@googlegroups.com> On Behalf Of esha dalal
Sent: 10 October 2024 16:16
To: cytogenetics-methods...@googlegroups.com
Subject:

 

Caution: This email did not come from CING. If you do not know the sender, do not click on any links, or attachments, or respond.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/3f3c6f0beed24e65949bf79e3e72b829%40cing.ac.cy.

----------
From: Mustafa Acar <mogu...@gmail.com>
Date: Thu, Oct 17, 2024 at 3:31 PM
To: Cytogenetics methods and trouble-shooting Forum <cytogenetics-methods...@googlegroups.com>

I thought it resembled a satellite. If you do NOR staining, it might help. Ectopic NOR has been reported on other non-acrocentric chromosomes.

(PMID: 10227407)

14 Ekim 2024 Pazartesi tarihinde saat 09:39:15 UTC+3 itibarıyla esha dalal şunları yazdı:

Hello everyone, 

I need comment regarding karyotype of a 27 yrs old female patient. 

There is a light band on chromosome 3p.

Please comment on how to interpret this. 

Thanks in advance. 

--

You received this message because you are subscribed to the Google Groups "Cytogenetics methods and trouble-shooting Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytogenetics-methods-and-t...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/4bff72fe-7d01-4d2f-b37d-5fccabc3e705n%40googlegroups.com.

----------
From: Istok828 <rus...@ukr.net>
Date: Fri, Oct 18, 2024 at 2:17 PM
To: Cytogenetics methods and trouble-shooting Forum <cytogenetics-methods...@googlegroups.com>

Hello, this is definitely an inversion.

четверг, 17 октября 2024 г. в 05:01:16 UTC-5, Mustafa Acar:

I thought it resembled a satellite. If you do NOR staining, it might help. Ectopic NOR has been reported on other non-acrocentric chromosomes.

(PMID: 10227407)

14 Ekim 2024 Pazartesi tarihinde saat 09:39:15 UTC+3 itibarıyla esha dalal şunları yazdı:

Hello everyone, 

I need comment regarding karyotype of a 27 yrs old female patient. 

There is a light band on chromosome 3p.

Please comment on how to interpret this. 

Thanks in advance. 

--

You received this message because you are subscribed to the Google Groups "Cytogenetics methods and trouble-shooting Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytogenetics-methods-and-t...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/de9e4e6b-bb71-42bc-ad35-894bd97ee8e6n%40googlegroups.com.

----------
From: Jasen Anderson <genema...@gmail.com>
Date: Sat, Oct 19, 2024 at 5:09 PM
To: <cytogenetics-methods...@googlegroups.com>

What are the clinical indications? Infertility or other phenotype? 

There's a number of things you can try. Whole paint 3 and also centromere chromosome 3 to exclude inversion first, the constriction is curious as is the p-terminus, looks a bit like satellites.

If not inversion from the centromere point of view, try NOR staining or Acro-p probe ( https://metasystems-probes.com/en/probes/xl/d-5440-050-or/ ) to see if that's satellites at the top,  If it isn't centromere 3 at the constriction,  it could be a Neocentromere. Just my initial thoughts. The abnormal chromosome looks bigger too, microarray would be a useful second round of testing to exclude extra material. 

Cheers

Jasen 

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CADEgMMC8a-PSKqfvQvdYCup4iNUVagCFDrmHYbiVpuNoYB4BPQ%40mail.gmail.com.

----------
From: esha dalal <esha...@gmail.com>
Date: Sat, Oct 19, 2024 at 5:10 PM
To: <cytogenetics-methods...@googlegroups.com>

Thank you all for your valuable suggestions.
The AMH level is very low (0.528 ng/ml) which is very low.

So before starting IVF cycle karyotype is recommended.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDQYfawZsdm0nceT58efQ8aXeguiow8pxCHP%2Bs95v0uusA%40mail.gmail.com.

----------
From: Jasen Anderson <genema...@gmail.com>
Date: Sun, Oct 20, 2024 at 5:00 PM
To: <cytogenetics-methods...@googlegroups.com>

Ok so likely unaffected phenotype apart from possible fertility issues. Keep us posted as to what steps you take to investigate and the outcome. 

Cheers

Jasen

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CADEgMMC%3D%3DUMHP--Xx5zfofcTB9sjgXJ3r_2Tnh3oRJcqZbzzkg%40mail.gmail.com.

----------
From: esha dalal <esha...@gmail.com>
Date: Mon, Oct 21, 2024 at 10:55 AM
To: <cytogenetics-methods...@googlegroups.com>

Sure

Thank you so much for your guidance.

Once again thank you so much to all

To view this discussion on the web visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDQwdcnxpzH-pj9iMpEppCxriE5FhoyLLka9EzzZYDMCWQ%40mail.gmail.com.

----------
From: esha dalal <esha...@gmail.com>
Date: Sat, Nov 9, 2024 at 3:08 PM
To: <cytogenetics-methods...@googlegroups.com>

Hello everyone, 

Can anyone please suggest Whole Exome Sequencing (WES) will be helpful in this case? 

Thanks in advance... 

Esha

To view this discussion visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDS00EttpiqQ1Fko%3DAxbzAy_JLt7iWjNLRmk9YgLbm_DzA%40mail.gmail.com.

----------
From: Jasen Anderson <genema...@gmail.com>
Date: Sun, Nov 10, 2024 at 3:15 PM
To: <cytogenetics-methods...@googlegroups.com>

I'd just go microarray first.. Cheaper. See what results are. 

Cheers

Jasen

To view this discussion visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CADEgMMA326BxaB69-Q%2BsVo3zdpuN56NSELTtm3gKVsJpnhO_DA%40mail.gmail.com.

----------
From: esha dalal <esha...@gmail.com>
Date: Mon, Nov 11, 2024 at 2:16 PM
To: <cytogenetics-methods...@googlegroups.com>

Sir, CMA is done and it's normal. 

So, I was thinking to do WES or can suggest PGT on embryo if patient choose IVF. 

And if patient wish for a natural pregnancy (as young age 27 yrs) , NIPT should be suggested in 1st trimester? 

Thanks

Esha

To view this discussion visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CAOMZTDTKjQi9PA_Qsvj3NRnf-t8Cwb_JKBTSDjqPf9LdM2SpKQ%40mail.gmail.com.

----------
From: Jasen Anderson <genema...@gmail.com>
Date: Mon, Nov 11, 2024 at 4:15 PM
To: <cytogenetics-methods...@googlegroups.com>

Hi. I'm not familiar with what extra information WES will provide in relation to the initial finding, if any, but as microarray did not detect anything, it would suggest that there's likely no consequences on a phenotype in any offspring that carry it. Did you attempt NOR banding or other techniques to exclude satellites from acrocentric chromosomes? Whole paint FISH? 

Cheers

Jasen

To view this discussion visit https://groups.google.com/d/msgid/cytogenetics-methods-and-trouble-shooting/CADEgMMCbp9fEAUq7j6X0PLC8jqEBMv8DCV%2BfHOoGJYkA0%3DVxGA%40mail.gmail.com.

----------
From: David Zhang <275792...@gmail.com>
Date: Tue, Nov 12, 2024 at 2:53 PM
To: Cytogenetics methods and trouble-shooting Forum <cytogenetics-methods...@googlegroups.com>

--